2-195897767-TAAAA-TAAAAAAA

Position:

• chr2-195897767-TAAAA-TAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6

The NM_018897.3(DNAH7):​c.4549-5_4549-3dupTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.000024 (0 hom., cov: 16)
  • Exomes 𝑓: 0.0011 (0 hom.)
• Consequence: DNAH7 NM_018897.3 splice_region, intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.179

Genes affected

DNAH7 (HGNC:18661): (dynein axonemal heavy chain 7) DNAH7 is a component of the inner dynein arm of ciliary axonemes (Zhang et al., 2002 [PubMed 11877439]).[supplied by OMIM, Mar 2008]

DNAH7 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP6: Variant 2-195897767-T-TAAA is Benign according to our data. Variant chr2-195897767-T-TAAA is described in ClinVar as [Likely_benign]. Clinvar id is 3048456.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DNAH7	NM_018897.3	c.4549-5_4549-3dupTTT		splice_region_variant, intron_variant		ENST00000312428.11	NP_061720.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNAH7	ENST00000312428.11	c.4549-5_4549-3dupTTT		splice_region_variant, intron_variant		1	NM_018897.3	ENSP00000311273.6
DNAH7	ENST00000475293.1	n.5482-5_5482-3dupTTT		splice_region_variant, intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0000240 AC: 3 AN: 124992 Hom.: 0 Cov.: 16

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000833

Gnomad ASJ AF: 0.000335

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000152

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00216 AC: 201 AN: 93048 Hom.: 0 AF XY: 0.00210 AC XY: 106 AN XY: 50580

Gnomad AFR exome AF: 0.00165

Gnomad AMR exome AF: 0.00357

Gnomad ASJ exome AF: 0.00131

Gnomad EAS exome AF: 0.00389

Gnomad SAS exome AF: 0.00235

Gnomad FIN exome AF: 0.00139

Gnomad NFE exome AF: 0.00186

Gnomad OTH exome AF: 0.00177

GnomAD4 exome AF: 0.00109 AC: 1114 AN: 1018680 Hom.: 0 Cov.: 0 AF XY: 0.00110 AC XY: 567 AN XY: 515010

Gnomad4 AFR exome AF: 0.000939

Gnomad4 AMR exome AF: 0.00299

Gnomad4 ASJ exome AF: 0.00114

Gnomad4 EAS exome AF: 0.00156

Gnomad4 SAS exome AF: 0.00270

Gnomad4 FIN exome AF: 0.00113

Gnomad4 NFE exome AF: 0.000908

Gnomad4 OTH exome AF: 0.000954

GnomAD4 genome AF: 0.0000240 AC: 3 AN: 124992 Hom.: 0 Cov.: 16 AF XY: 0.0000167 AC XY: 1 AN XY: 59848

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000833

Gnomad4 ASJ AF: 0.000335

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000152

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

DNAH7-related disorder Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 27, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs61502519; hg19: chr2-196762491;