7-119327903-A-T

Variant names:

• chr7-119327903-A-T
• rs308106

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 0.857 in 149,436 control chromosomes in the GnomAD database, including 57,593 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 0.86 (57593 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.858 AC: 128086 AN: 149360 Hom.: 57601 Cov.: 25

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.961

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.857 AC: 128093 AN: 149436 Hom.: 57593 Cov.: 25 AF XY: 0.861 AC XY: 62690 AN XY: 72832

African (AFR) AF: 0.548 AC: 22056 AN: 40216

American (AMR) AF: 0.910 AC: 13662 AN: 15012

Ashkenazi Jewish (ASJ) AF: 0.996 AC: 3453 AN: 3466

East Asian (EAS) AF: 0.902 AC: 4567 AN: 5064

South Asian (SAS) AF: 0.972 AC: 4627 AN: 4758

European-Finnish (FIN) AF: 0.985 AC: 9742 AN: 9892

Middle Eastern (MID) AF: 0.957 AC: 270 AN: 282

European-Non Finnish (NFE) AF: 0.988 AC: 66975 AN: 67758

Other (OTH) AF: 0.886 AC: 1841 AN: 2078

Alfa AF: 0.909 Hom.: 8066

Bravo AF: 0.833

Asia WGS AF: 0.875 AC: 3038 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.53
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs308106; hg19: chr7-118967957;