7-39613627-T-G

Variant names:

• chr7-39613627-T-G
• rs10486799

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0332

Gnomad4 ASJ AF: 0.0982

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.0836

Gnomad4 FIN AF: 0.0738

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0633 Hom.: 470

Bravo AF: 0.0472

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486799; hg19: chr7-39653226;