rs4947638

Variant names:

• chr7-51759659-G-A
• rs4947638

Your query was ambiguous. Multiple possible variants found:

• chr7-51759659-G-A
• chr7-51759659-G-C

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 0.219 in 152,140 control chromosomes in the GnomAD database, including 3,722 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 0.22 (3722 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33245 AN: 152022 Hom.: 3721 Cov.: 33

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.219 AC: 33259 AN: 152140 Hom.: 3722 Cov.: 33 AF XY: 0.216 AC XY: 16036 AN XY: 74380

African (AFR) AF: 0.214 AC: 8889 AN: 41486

American (AMR) AF: 0.262 AC: 4007 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1357 AN: 5154

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1237 AN: 10604

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14548 AN: 67996

Other (OTH) AF: 0.249 AC: 526 AN: 2114

Alfa AF: 0.229 Hom.: 6994

Bravo AF: 0.231

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.66
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4947638; hg19: chr7-51827355;