7-138304009-A-G

Variant names:

• chr7-138304009-A-G
• rs410156

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 0.81 in 148,492 control chromosomes in the GnomAD database, including 49,540 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 0.81 (49540 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 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: 0.810 AC: 120215 AN: 148374 Hom.: 49486 Cov.: 23

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.810 AC: 120329 AN: 148492 Hom.: 49540 Cov.: 23 AF XY: 0.803 AC XY: 57936 AN XY: 72136

African (AFR) AF: 0.951 AC: 38235 AN: 40208

American (AMR) AF: 0.710 AC: 10321 AN: 14530

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2863 AN: 3456

East Asian (EAS) AF: 0.559 AC: 2819 AN: 5046

South Asian (SAS) AF: 0.809 AC: 3653 AN: 4516

European-Finnish (FIN) AF: 0.711 AC: 7141 AN: 10048

Middle Eastern (MID) AF: 0.826 AC: 238 AN: 288

European-Non Finnish (NFE) AF: 0.780 AC: 52625 AN: 67472

Other (OTH) AF: 0.816 AC: 1653 AN: 2026

Alfa AF: 0.793 Hom.: 5896

Bravo AF: 0.817

Asia WGS AF: 0.735 AC: 2558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.70
DANN	Benign	0.57
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs410156; hg19: chr7-137988754;