7-119932337-C-T

Variant names:

• chr7-119932337-C-T
• rs10231641

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 0.835 in 151,886 control chromosomes in the GnomAD database, including 53,530 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 0.84 (53530 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

ACMG classification

Verdict is Benign. Variant got -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 = 0.975 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: 0.835 AC: 126708 AN: 151768 Hom.: 53466 Cov.: 30

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.835 AC: 126834 AN: 151886 Hom.: 53530 Cov.: 30 AF XY: 0.834 AC XY: 61863 AN XY: 74204

Gnomad4 AFR AF: 0.952

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.832

Alfa AF: 0.786 Hom.: 46757

Bravo AF: 0.845

Asia WGS AF: 0.926 AC: 3210 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10231641; hg19: chr7-119572391;