rs7596121

Positions:

• chr2-195782165-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018897.3(DNAH7):​c.10879-4180A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,234 control chromosomes in the GnomAD database, including 2,207 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (2207 hom., cov: 32)
• Consequence: DNAH7 NM_018897.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH7	NM_018897.3	c.10879-4180A>G		intron_variant		ENST00000312428.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH7	ENST00000312428.11	c.10879-4180A>G		intron_variant		1	NM_018897.3	P1
DNAH7	ENST00000409063.5	c.328-4180A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23513 AN: 152116 Hom.: 2205 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0869

Gnomad FIN AF: 0.0804

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.155 AC: 23534 AN: 152234 Hom.: 2207 Cov.: 32 AF XY: 0.150 AC XY: 11147 AN XY: 74458

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0870

Gnomad4 FIN AF: 0.0804

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.161

Alfa AF: 0.138 Hom.: 305

Bravo AF: 0.163

Asia WGS AF: 0.0580 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.8
DANN	Benign	0.87

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: rs7596121; hg19: chr2-196646889; COSMIC: COSV56755322;