rs1372894

Variant names:

• chr4-170663267-A-G
• rs1372894

Your query was ambiguous. Multiple possible variants found:

• chr4-170663267-A-G
• chr4-170663267-A-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 0.459 in 151,948 control chromosomes in the GnomAD database, including 21,002 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 0.46 (21002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 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: 0.459 AC: 69657 AN: 151830 Hom.: 20947 Cov.: 32

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.459 AC: 69771 AN: 151948 Hom.: 21002 Cov.: 32 AF XY: 0.448 AC XY: 33261 AN XY: 74272

African (AFR) AF: 0.847 AC: 35100 AN: 41454

American (AMR) AF: 0.502 AC: 7652 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3468

East Asian (EAS) AF: 0.104 AC: 538 AN: 5166

South Asian (SAS) AF: 0.243 AC: 1174 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1691 AN: 10584

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20853 AN: 67920

Other (OTH) AF: 0.450 AC: 946 AN: 2102

Alfa AF: 0.183 Hom.: 325

Bravo AF: 0.502

Asia WGS AF: 0.230 AC: 803 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.070
DANN	Benign	0.44
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1372894; hg19: chr4-171584418;