chr7-39613627-T-G

Variant names:

• chr7-39613627-T-G
• rs10486799

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 0.0525 in 152,344 control chromosomes in the GnomAD database, including 285 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 0.052 (285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 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: 0.0526 AC: 8010 AN: 152226 Hom.: 285 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0844

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0525 AC: 7997 AN: 152344 Hom.: 285 Cov.: 32 AF XY: 0.0533 AC XY: 3969 AN XY: 74488

African (AFR) AF: 0.0112 AC: 467 AN: 41594

American (AMR) AF: 0.0332 AC: 508 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0982 AC: 341 AN: 3472

East Asian (EAS) AF: 0.121 AC: 625 AN: 5180

South Asian (SAS) AF: 0.0836 AC: 404 AN: 4832

European-Finnish (FIN) AF: 0.0738 AC: 783 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0693 AC: 4711 AN: 68028

Other (OTH) AF: 0.0610 AC: 129 AN: 2116

Alfa AF: 0.0616 Hom.: 550

Bravo AF: 0.0472

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.3
DANN	Benign	0.62
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10486799; hg19: chr7-39653226;