rs16872911

Variant names:

• chr7-21749821-T-G
• rs16872911
• NM_001277115.2:c.8797+20T>G

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_Moderate BP6_Very_Strong BA1

The NM_001277115.2(DNAH11):​c.8797+20T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00173 in 1,612,870 control chromosomes in the GnomAD database, including 111 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0028 (17 hom., cov: 32)
  • Exomes 𝑓: 0.0016 (94 hom.)
• Consequence: DNAH11 NM_001277115.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.0580

Genes affected

DNAH11 (HGNC:2942): (dynein axonemal heavy chain 11) This gene encodes a ciliary outer dynein arm protein and is a member of the dynein heavy chain family. It is a microtubule-dependent motor ATPase and has been reported to be involved in the movement of respiratory cilia. Mutations in this gene have been implicated in causing Kartagener Syndrome (a combination of situs inversus totalis and Primary Ciliary Dyskinesia (PCD), also called Immotile Cilia Syndrome 1 (ICS1)) and male sterility. [provided by RefSeq, Mar 2013]

ACMG classification

Our verdict: Benign. The variant received -18 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BP6: Variant 7-21749821-T-G is Benign according to our data. Variant chr7-21749821-T-G is described in ClinVar as [Benign]. Clinvar id is 257936.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-21749821-T-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DNAH11	NM_001277115.2	c.8797+20T>G		intron_variant	Intron 53 of 81	ENST00000409508.8	NP_001264044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DNAH11	ENST00000409508.8	c.8797+20T>G		intron_variant	Intron 53 of 81	5	NM_001277115.2	ENSP00000475939.1

Frequencies

GnomAD3 genomes AF: 0.00281 AC: 428 AN: 152176 Hom.: 17 Cov.: 32

Gnomad AFR AF: 0.000410

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000524

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0740

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000735

Gnomad OTH AF: 0.00334

GnomAD2 exomes AF: 0.00639 AC: 1582 AN: 247648 AF XY: 0.00580

Gnomad AFR exome AF: 0.000194

Gnomad AMR exome AF: 0.000292

Gnomad ASJ exome AF: 0.000100

Gnomad EAS exome AF: 0.0855

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000445

Gnomad OTH exome AF: 0.00233

GnomAD4 exome AF: 0.00162 AC: 2373 AN: 1460576 Hom.: 94 Cov.: 30 AF XY: 0.00155 AC XY: 1127 AN XY: 726378

Gnomad4 AFR exome AF: 0.000269 AC: 9 AN: 33456

Gnomad4 AMR exome AF: 0.000224 AC: 10 AN: 44622

Gnomad4 ASJ exome AF: 0.0000383 AC: 1 AN: 26096

Gnomad4 EAS exome AF: 0.0502 AC: 1990 AN: 39674

Gnomad4 SAS exome AF: 0.000570 AC: 49 AN: 85972

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 53392

Gnomad4 NFE exome AF: 0.0000405 AC: 45 AN: 1111278

Gnomad4 Remaining exome AF: 0.00443 AC: 267 AN: 60326

GnomAD4 genome AF: 0.00279 AC: 425 AN: 152294 Hom.: 17 Cov.: 32 AF XY: 0.00309 AC XY: 230 AN XY: 74474

Gnomad4 AFR AF: 0.000409 AC: 0.000408988 AN: 0.000408988

Gnomad4 AMR AF: 0.000523 AC: 0.000523013 AN: 0.000523013

Gnomad4 ASJ AF: 0.00 AC: 0 AN: 0

Gnomad4 EAS AF: 0.0736 AC: 0.0736374 AN: 0.0736374

Gnomad4 SAS AF: 0.00145 AC: 0.00144988 AN: 0.00144988

Gnomad4 FIN AF: 0.00 AC: 0 AN: 0

Gnomad4 NFE AF: 0.0000735 AC: 0.00007351 AN: 0.00007351

Gnomad4 OTH AF: 0.00331 AC: 0.00330813 AN: 0.00330813

Alfa AF: 0.000598 Hom.: 0

Bravo AF: 0.00347

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Primary ciliary dyskinesia Benign:1

Feb 01, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Benign:1

May 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	13
DANN	Benign	0.79
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

Publications

LitVar

Other links and lift over

dbSNP: rs16872911; hg19: chr7-21789439; COSMIC: COSV60980594; COSMIC: COSV60980594;