13-40927691-T-C

Variant names:

• chr13-40927691-T-C
• rs9532670

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 0.525 in 151,682 control chromosomes in the GnomAD database, including 24,440 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 0.52 (24440 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 6 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 = 0.67 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: 0.525 AC: 79614 AN: 151564 Hom.: 24446 Cov.: 29

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.647

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.525 AC: 79610 AN: 151682 Hom.: 24440 Cov.: 29 AF XY: 0.529 AC XY: 39227 AN XY: 74118

African (AFR) AF: 0.215 AC: 8899 AN: 41354

American (AMR) AF: 0.644 AC: 9823 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2168 AN: 3460

East Asian (EAS) AF: 0.162 AC: 831 AN: 5138

South Asian (SAS) AF: 0.568 AC: 2733 AN: 4810

European-Finnish (FIN) AF: 0.693 AC: 7246 AN: 10462

Middle Eastern (MID) AF: 0.641 AC: 186 AN: 290

European-Non Finnish (NFE) AF: 0.675 AC: 45834 AN: 67904

Other (OTH) AF: 0.559 AC: 1178 AN: 2106

Alfa AF: 0.573 Hom.: 4339

Bravo AF: 0.510

Asia WGS AF: 0.333 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9532670; hg19: chr13-41501827;