rs410156

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;