chr4-4261852-A-C

Variant names:

• chr4-4261852-A-C
• rs2920228

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 0.652 in 152,156 control chromosomes in the GnomAD database, including 32,738 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 0.65 (32738 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.704 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: 0.652 AC: 99147 AN: 152038 Hom.: 32692 Cov.: 34

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.652 AC: 99245 AN: 152156 Hom.: 32738 Cov.: 34 AF XY: 0.652 AC XY: 48469 AN XY: 74392

African (AFR) AF: 0.571 AC: 23696 AN: 41496

American (AMR) AF: 0.611 AC: 9336 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2506 AN: 3470

East Asian (EAS) AF: 0.506 AC: 2617 AN: 5174

South Asian (SAS) AF: 0.633 AC: 3060 AN: 4832

European-Finnish (FIN) AF: 0.722 AC: 7630 AN: 10574

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48252 AN: 68004

Other (OTH) AF: 0.656 AC: 1386 AN: 2114

Alfa AF: 0.683 Hom.: 54161

Bravo AF: 0.637

Asia WGS AF: 0.604 AC: 2102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.30
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2920228; hg19: chr4-4263579;