rs4707930

Variant names:

• chr6-71696616-T-G
• rs4707930

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 0.687 in 152,014 control chromosomes in the GnomAD database, including 36,863 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 0.69 (36863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104425 AN: 151896 Hom.: 36865 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.687 AC: 104447 AN: 152014 Hom.: 36863 Cov.: 32 AF XY: 0.687 AC XY: 51054 AN XY: 74306

African (AFR) AF: 0.534 AC: 22125 AN: 41424

American (AMR) AF: 0.636 AC: 9708 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2822 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2788 AN: 5168

South Asian (SAS) AF: 0.769 AC: 3704 AN: 4818

European-Finnish (FIN) AF: 0.797 AC: 8433 AN: 10584

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52573 AN: 67970

Other (OTH) AF: 0.695 AC: 1466 AN: 2108

Alfa AF: 0.730 Hom.: 63106

Bravo AF: 0.662

Asia WGS AF: 0.604 AC: 2101 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.59
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs4707930; hg19: chr6-72406319;