rs13264338

chr8-23591788-C-Achr8-23591788-C-Gchr8-23591788-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 0.627 in 151,942 control chromosomes in the GnomAD database, including 30,797 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 0.63 (30797 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.626 AC: 95094 AN: 151824 Hom.: 30753 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.627 AC: 95202 AN: 151942 Hom.: 30797 Cov.: 32 AF XY: 0.634 AC XY: 47063 AN XY: 74240

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.597

Alfa AF: 0.565 Hom.: 13916

Bravo AF: 0.633

Asia WGS AF: 0.706 AC: 2455 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	2.2
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13264338; hg19: chr8-23449301;