rs4654438

Variant names:

• chr1-4499841-T-C
• rs4654438

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 0.489 in 151,976 control chromosomes in the GnomAD database, including 18,652 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 0.49 (18652 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.489 AC: 74240 AN: 151858 Hom.: 18622 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.489 AC: 74312 AN: 151976 Hom.: 18652 Cov.: 32 AF XY: 0.490 AC XY: 36401 AN XY: 74284

African (AFR) AF: 0.435 AC: 18024 AN: 41456

American (AMR) AF: 0.608 AC: 9275 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1829 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4158 AN: 5148

South Asian (SAS) AF: 0.419 AC: 2017 AN: 4812

European-Finnish (FIN) AF: 0.451 AC: 4763 AN: 10568

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32466 AN: 67950

Other (OTH) AF: 0.513 AC: 1078 AN: 2102

Alfa AF: 0.500 Hom.: 8599

Bravo AF: 0.506

Asia WGS AF: 0.588 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4654438; hg19: chr1-4559901; COSMIC: COSV59919689;