rs4851531

Variant names:

• chr2-102032147-C-T
• rs4851531

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 0.471 in 151,904 control chromosomes in the GnomAD database, including 17,396 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 0.47 (17396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 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: 0.471 AC: 71491 AN: 151786 Hom.: 17357 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.471 AC: 71578 AN: 151904 Hom.: 17396 Cov.: 32 AF XY: 0.478 AC XY: 35513 AN XY: 74232

African (AFR) AF: 0.555 AC: 23003 AN: 41414

American (AMR) AF: 0.481 AC: 7337 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2704 AN: 5172

South Asian (SAS) AF: 0.368 AC: 1770 AN: 4814

European-Finnish (FIN) AF: 0.599 AC: 6300 AN: 10524

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27773 AN: 67932

Other (OTH) AF: 0.433 AC: 913 AN: 2108

Alfa AF: 0.416 Hom.: 18524

Bravo AF: 0.470

Asia WGS AF: 0.464 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.038
DANN	Benign	0.41
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4851531; hg19: chr2-102648609; COSMIC: COSV60206452;