4-130216606-T-C

Variant names:

• chr4-130216606-T-C
• rs1024020

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 0.714 in 151,984 control chromosomes in the GnomAD database, including 39,428 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 0.71 (39428 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.818
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 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: 0.714 AC: 108443 AN: 151866 Hom.: 39416 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.714 AC: 108499 AN: 151984 Hom.: 39428 Cov.: 32 AF XY: 0.710 AC XY: 52748 AN XY: 74248

African (AFR) AF: 0.618 AC: 25636 AN: 41482

American (AMR) AF: 0.702 AC: 10688 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2283 AN: 3470

East Asian (EAS) AF: 0.458 AC: 2361 AN: 5158

South Asian (SAS) AF: 0.628 AC: 3024 AN: 4818

European-Finnish (FIN) AF: 0.752 AC: 7921 AN: 10538

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54193 AN: 67978

Other (OTH) AF: 0.724 AC: 1527 AN: 2108

Alfa AF: 0.761 Hom.: 190375

Bravo AF: 0.707

Asia WGS AF: 0.557 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.84
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1024020; hg19: chr4-131137761;