chr13-31364049-A-C

Position:

• chr13-31364049-A-C

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 0.667 in 152,174 control chromosomes in the GnomAD database, including 34,904 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 0.67 (34904 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101467 AN: 152056 Hom.: 34903 Cov.: 34

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.667 AC: 101520 AN: 152174 Hom.: 34904 Cov.: 34 AF XY: 0.663 AC XY: 49294 AN XY: 74388

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.676

Alfa AF: 0.743 Hom.: 70208

Bravo AF: 0.660

Asia WGS AF: 0.646 AC: 2245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.9
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1326306; hg19: chr13-31938186;