rs11077379

Variant names:

• chr17-78532749-G-A
• rs11077379
• NM_173628.4:c.2860-13C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-78532749-G-A
• chr17-78532749-G-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_173628.4(DNAH17):​c.2860-13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 1,575,886 control chromosomes in the GnomAD database, including 216,562 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.52 (20438 hom., cov: 31)
  • Exomes 𝑓: 0.52 (196124 hom.)
• Consequence: DNAH17 NM_173628.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 0.320
• Publications: 8 publications found

Genes affected

DNAH17 (HGNC:2946): (dynein axonemal heavy chain 17) Dyneins are microtubule-associated motor protein complexes composed of several heavy, light, and intermediate chains. DNAH17 is a heavy chain associated with axonemal dynein (Milisav and Affara, 1998 [PubMed 9545504]).[supplied by OMIM, Mar 2008]

RN7SL454P (HGNC:46470): (RNA, 7SL, cytoplasmic 454, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 17-78532749-G-A is Benign according to our data. Variant chr17-78532749-G-A is described in ClinVar as Benign. ClinVar VariationId is 402698.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH17	NM_173628.4	c.2860-13C>T		intron_variant	Intron 19 of 80	ENST00000389840.7	NP_775899.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH17	ENST00000389840.7	c.2860-13C>T		intron_variant	Intron 19 of 80	5	NM_173628.4	ENSP00000374490.6
RN7SL454P	ENST00000492744.3	n.*64C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78317 AN: 151756 Hom.: 20429 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.525

GnomAD2 exomes AF: 0.496 AC: 101048 AN: 203670 AF XY: 0.500

Gnomad AFR exome AF: 0.474

Gnomad AMR exome AF: 0.388

Gnomad ASJ exome AF: 0.539

Gnomad EAS exome AF: 0.485

Gnomad FIN exome AF: 0.560

Gnomad NFE exome AF: 0.532

Gnomad OTH exome AF: 0.522

GnomAD4 exome AF: 0.524 AC: 746354 AN: 1424012 Hom.: 196124 Cov.: 40 AF XY: 0.523 AC XY: 368405 AN XY: 704716

African (AFR) AF: 0.485 AC: 15852 AN: 32662

American (AMR) AF: 0.393 AC: 15718 AN: 39950

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 13362 AN: 24868

East Asian (EAS) AF: 0.497 AC: 19261 AN: 38762

South Asian (SAS) AF: 0.450 AC: 36546 AN: 81192

European-Finnish (FIN) AF: 0.565 AC: 28898 AN: 51168

Middle Eastern (MID) AF: 0.556 AC: 3093 AN: 5562

European-Non Finnish (NFE) AF: 0.534 AC: 582669 AN: 1090830

Other (OTH) AF: 0.525 AC: 30955 AN: 59018

GnomAD4 genome AF: 0.516 AC: 78359 AN: 151874 Hom.: 20438 Cov.: 31 AF XY: 0.514 AC XY: 38154 AN XY: 74224

African (AFR) AF: 0.491 AC: 20295 AN: 41370

American (AMR) AF: 0.438 AC: 6689 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1813 AN: 3470

East Asian (EAS) AF: 0.490 AC: 2530 AN: 5158

South Asian (SAS) AF: 0.441 AC: 2121 AN: 4814

European-Finnish (FIN) AF: 0.573 AC: 6039 AN: 10544

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36931 AN: 67950

Other (OTH) AF: 0.522 AC: 1100 AN: 2106

Alfa AF: 0.517 Hom.: 2882

Bravo AF: 0.505

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

May 04, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.27
DANN	Benign	0.74
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11077379; hg19: chr17-76528831; COSMIC: COSV67752462; COSMIC: COSV67752462;