rs2441701

Positions:

• chr8-101157875-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 0.655 in 152,074 control chromosomes in the GnomAD database, including 34,543 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 0.66 (34543 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.101157875C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99548 AN: 151956 Hom.: 34476 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.655 AC: 99677 AN: 152074 Hom.: 34543 Cov.: 32 AF XY: 0.654 AC XY: 48572 AN XY: 74302

Gnomad4 AFR AF: 0.893

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.608

Alfa AF: 0.564 Hom.: 33613

Bravo AF: 0.671

Asia WGS AF: 0.558 AC: 1939 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	0.36
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2441701; hg19: chr8-102170103;