rs13272414

chr8-56271050-C-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 0.156 in 152,084 control chromosomes in the GnomAD database, including 1,891 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 0.16 (1891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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: 0.156 AC: 23683 AN: 151966 Hom.: 1888 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.156 AC: 23698 AN: 152084 Hom.: 1891 Cov.: 32 AF XY: 0.154 AC XY: 11438 AN XY: 74344

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0601

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.171

Alfa AF: 0.147 Hom.: 837

Bravo AF: 0.160

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.95
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13272414; hg19: chr8-57183609;