chr7-23704930-C-A

Variant names:

• chr7-23704930-C-A
• rs6974500

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.574 in 151,902 control chromosomes in the GnomAD database, including 26,149 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 0.57 (26149 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87173 AN: 151784 Hom.: 26164 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.574 AC: 87173 AN: 151902 Hom.: 26149 Cov.: 31 AF XY: 0.577 AC XY: 42871 AN XY: 74242

African (AFR) AF: 0.382 AC: 15822 AN: 41380

American (AMR) AF: 0.642 AC: 9805 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3470

East Asian (EAS) AF: 0.641 AC: 3315 AN: 5174

South Asian (SAS) AF: 0.696 AC: 3342 AN: 4804

European-Finnish (FIN) AF: 0.660 AC: 6948 AN: 10534

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43681 AN: 67958

Other (OTH) AF: 0.576 AC: 1218 AN: 2114

Alfa AF: 0.628 Hom.: 59703

Bravo AF: 0.560

Asia WGS AF: 0.651 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.30
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6974500; hg19: chr7-23744549;