rs4675872

chr2-240884036-G-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 0.436 in 151,590 control chromosomes in the GnomAD database, including 14,822 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 0.44 (14822 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.621

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66071 AN: 151472 Hom.: 14793 Cov.: 30

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.436 AC: 66134 AN: 151590 Hom.: 14822 Cov.: 30 AF XY: 0.434 AC XY: 32152 AN XY: 74080

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.413

Alfa AF: 0.407 Hom.: 5473

Bravo AF: 0.440

Asia WGS AF: 0.458 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.6
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4675872; hg19: chr2-241823453;