7-119318926-T-G

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 0.854 in 152,028 control chromosomes in the GnomAD database, including 58,347 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 0.85 (58347 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.855 AC: 129851 AN: 151910 Hom.: 58343 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.971

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.854 AC: 129888 AN: 152028 Hom.: 58347 Cov.: 33 AF XY: 0.859 AC XY: 63828 AN XY: 74332

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.996

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.972

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.884

Alfa AF: 0.959 Hom.: 23907

Bravo AF: 0.833

Asia WGS AF: 0.875 AC: 3030 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.60
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs308143; hg19: chr7-118958980;