rs281757

Variant names:

• chr8-107619754-T-C
• rs281757

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 0.64 in 152,010 control chromosomes in the GnomAD database, including 31,588 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 0.64 (31588 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.737 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: 0.641 AC: 97294 AN: 151892 Hom.: 31574 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.796

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.640 AC: 97350 AN: 152010 Hom.: 31588 Cov.: 32 AF XY: 0.643 AC XY: 47785 AN XY: 74284

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.690

Alfa AF: 0.668 Hom.: 16304

Bravo AF: 0.628

Asia WGS AF: 0.697 AC: 2421 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.42
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs281757; hg19: chr8-108631982;