7-119932337-C-T

Position:

• chr7-119932337-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;