rs4713580

Variant names:

• chr6-32692217-C-T
• rs4713580

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 0.536 in 151,954 control chromosomes in the GnomAD database, including 22,307 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 0.54 (22307 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 12 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 (EAS) allele frequency at 95% confidence interval = 0.634 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: 0.536 AC: 81431 AN: 151836 Hom.: 22286 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.536 AC: 81508 AN: 151954 Hom.: 22307 Cov.: 31 AF XY: 0.541 AC XY: 40182 AN XY: 74282

African (AFR) AF: 0.524 AC: 21712 AN: 41416

American (AMR) AF: 0.634 AC: 9691 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2130 AN: 3468

East Asian (EAS) AF: 0.652 AC: 3371 AN: 5168

South Asian (SAS) AF: 0.417 AC: 2004 AN: 4804

European-Finnish (FIN) AF: 0.616 AC: 6496 AN: 10554

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34109 AN: 67950

Other (OTH) AF: 0.555 AC: 1170 AN: 2108

Alfa AF: 0.530 Hom.: 8292

Bravo AF: 0.543

Asia WGS AF: 0.596 AC: 2078 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	12
DANN	Benign	0.70
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4713580; hg19: chr6-32659994;