rs1874572

Variant names:

• chr4-145588818-T-G
• rs1874572

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 0.342 in 151,798 control chromosomes in the GnomAD database, including 9,042 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 0.34 (9042 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 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: 0.342 AC: 51825 AN: 151680 Hom.: 9039 Cov.: 30

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.342 AC: 51845 AN: 151798 Hom.: 9042 Cov.: 30 AF XY: 0.339 AC XY: 25143 AN XY: 74194

African (AFR) AF: 0.402 AC: 16653 AN: 41400

American (AMR) AF: 0.281 AC: 4277 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1466 AN: 5164

South Asian (SAS) AF: 0.283 AC: 1353 AN: 4778

European-Finnish (FIN) AF: 0.348 AC: 3665 AN: 10538

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 22074 AN: 67920

Other (OTH) AF: 0.320 AC: 672 AN: 2102

Alfa AF: 0.328 Hom.: 33689

Bravo AF: 0.339

Asia WGS AF: 0.254 AC: 883 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.43
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1874572; hg19: chr4-146509970;