rs17254431

Positions:

• chr8-13774507-A-G
• chr8-13774507-A-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 0.117 in 150,670 control chromosomes in the GnomAD database, including 1,413 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 0.12 (1413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.488

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.168 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: 0.117 AC: 17686 AN: 150554 Hom.: 1413 Cov.: 32

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.117 AC: 17687 AN: 150670 Hom.: 1413 Cov.: 32 AF XY: 0.118 AC XY: 8722 AN XY: 73668

Gnomad4 AFR AF: 0.0616

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.0811

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.140

Alfa AF: 0.0601 Hom.: 88

Bravo AF: 0.119

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17254431; hg19: chr8-13632016;