rs4675872

Variant names:

• chr2-240884036-G-T
• rs4675872

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 0.436 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.511 AC: 21069 AN: 41226

American (AMR) AF: 0.400 AC: 6101 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3468

East Asian (EAS) AF: 0.586 AC: 3013 AN: 5144

South Asian (SAS) AF: 0.321 AC: 1540 AN: 4794

European-Finnish (FIN) AF: 0.438 AC: 4600 AN: 10514

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27388 AN: 67886

Other (OTH) AF: 0.413 AC: 870 AN: 2106

Alfa AF: 0.407 Hom.: 6141

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
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs4675872; hg19: chr2-241823453;