rs4663247

Variant names:

• chr2-237285479-A-T
• rs4663247

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 0.533 in 152,046 control chromosomes in the GnomAD database, including 21,808 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 0.53 (21808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.605 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: 0.533 AC: 80942 AN: 151928 Hom.: 21765 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.533 AC: 81052 AN: 152046 Hom.: 21808 Cov.: 32 AF XY: 0.537 AC XY: 39897 AN XY: 74318

African (AFR) AF: 0.577 AC: 23910 AN: 41470

American (AMR) AF: 0.602 AC: 9207 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1640 AN: 3472

East Asian (EAS) AF: 0.610 AC: 3153 AN: 5172

South Asian (SAS) AF: 0.624 AC: 3006 AN: 4820

European-Finnish (FIN) AF: 0.496 AC: 5239 AN: 10562

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33355 AN: 67952

Other (OTH) AF: 0.509 AC: 1073 AN: 2108

Alfa AF: 0.519 Hom.: 2868

Bravo AF: 0.537

Asia WGS AF: 0.626 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4663247; hg19: chr2-238194122; COSMIC: COSV107166620;