10-131557326-A-C

Variant names:

• chr10-131557326-A-C
• rs7071307

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 0.606 in 151,342 control chromosomes in the GnomAD database, including 27,921 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 0.61 (27921 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 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: 0.606 AC: 91607 AN: 151220 Hom.: 27897 Cov.: 27

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.606 AC: 91677 AN: 151342 Hom.: 27921 Cov.: 27 AF XY: 0.607 AC XY: 44876 AN XY: 73914

African (AFR) AF: 0.669 AC: 27540 AN: 41190

American (AMR) AF: 0.518 AC: 7871 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2550 AN: 3470

East Asian (EAS) AF: 0.656 AC: 3359 AN: 5122

South Asian (SAS) AF: 0.643 AC: 3063 AN: 4762

European-Finnish (FIN) AF: 0.608 AC: 6344 AN: 10430

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38841 AN: 67868

Other (OTH) AF: 0.607 AC: 1274 AN: 2100

Alfa AF: 0.587 Hom.: 77405

Bravo AF: 0.601

Asia WGS AF: 0.650 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.51
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7071307; hg19: chr10-133355589;