rs893762

Variant names:

• chr1-47654317-C-T
• rs893762

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0667 in 152,272 control chromosomes in the GnomAD database, including 343 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 0.067 (343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.104 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: 0.0667 AC: 10146 AN: 152154 Hom.: 343 Cov.: 32

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0539

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0689

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

GnomAD4 genome AF: 0.0667 AC: 10160 AN: 152272 Hom.: 343 Cov.: 32 AF XY: 0.0671 AC XY: 4998 AN XY: 74468

African (AFR) AF: 0.0556 AC: 2309 AN: 41560

American (AMR) AF: 0.0482 AC: 738 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0982 AC: 341 AN: 3472

East Asian (EAS) AF: 0.112 AC: 579 AN: 5182

South Asian (SAS) AF: 0.108 AC: 519 AN: 4822

European-Finnish (FIN) AF: 0.0539 AC: 572 AN: 10614

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4806 AN: 68012

Other (OTH) AF: 0.0687 AC: 145 AN: 2112

Alfa AF: 0.0681 Hom.: 666

Bravo AF: 0.0647

Asia WGS AF: 0.110 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.5
DANN	Benign	0.49
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs893762; hg19: chr1-48119989;