rs410156

Variant names:

• chr7-138304009-A-G
• rs410156

Your query was ambiguous. Multiple possible variants found:

• chr7-138304009-A-G
• chr7-138304009-A-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 0.81 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.951

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.816

Alfa AF: 0.787 Hom.: 5558

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs410156; hg19: chr7-137988754;