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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.450

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1372894; hg19: chr4-171584418;