rs1503874

Variant names:

• chr4-18127018-G-A
• rs1503874

Your query was ambiguous. Multiple possible variants found:

• chr4-18127018-G-A
• chr4-18127018-G-C
• chr4-18127018-G-T

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 0.384 in 151,928 control chromosomes in the GnomAD database, including 11,403 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 0.38 (11403 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• 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 (SAS) allele frequency at 95% confidence interval = 0.505 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: 0.384 AC: 58349 AN: 151810 Hom.: 11378 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.384 AC: 58407 AN: 151928 Hom.: 11403 Cov.: 32 AF XY: 0.385 AC XY: 28573 AN XY: 74256

African (AFR) AF: 0.428 AC: 17746 AN: 41428

American (AMR) AF: 0.382 AC: 5831 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5174

South Asian (SAS) AF: 0.522 AC: 2506 AN: 4804

European-Finnish (FIN) AF: 0.323 AC: 3407 AN: 10548

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 25017 AN: 67934

Other (OTH) AF: 0.373 AC: 789 AN: 2114

Alfa AF: 0.385 Hom.: 6282

Bravo AF: 0.387

Asia WGS AF: 0.409 AC: 1423 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	7.3
DANN	Benign	0.62
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs1503874; hg19: chr4-18128641;