rs4663247

Positions:

• chr2-237285479-A-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 0.533 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.509

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4663247; hg19: chr2-238194122;