rs6434804

chr2-195899669-T-G

Variant summary

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

The NM_018897.3(DNAH7):c.4548+613A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,166 control chromosomes in the GnomAD database, including 2,947 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 0.17 (2947 hom., cov: 32)
• Consequence: DNAH7 NM_018897.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.884

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=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DNAH7	NM_018897.3	c.4548+613A>C		intron_variant		ENST00000312428.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DNAH7	ENST00000312428.11	c.4548+613A>C		intron_variant		1	NM_018897.3	P1
DNAH7	ENST00000475293.1	n.5481+613A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26153 AN: 152048 Hom.: 2942 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.0801

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.172 AC: 26196 AN: 152166 Hom.: 2947 Cov.: 32 AF XY: 0.167 AC XY: 12443 AN XY: 74396

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0884

Gnomad4 FIN AF: 0.0801

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.174

Alfa AF: 0.149 Hom.: 271

Bravo AF: 0.183

Asia WGS AF: 0.0620 AC: 215 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	12
Dann	Benign	0.83

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: rs6434804; hg19: chr2-196764393;