1-17488937-G-A

Variant names:

• chr1-17488937-G-A
• rs4387213

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 0.315 in 144,722 control chromosomes in the GnomAD database, including 7,542 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 0.31 (7542 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.339 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: 0.315 AC: 45518 AN: 144606 Hom.: 7538 Cov.: 23

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0873

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.315 AC: 45542 AN: 144722 Hom.: 7542 Cov.: 23 AF XY: 0.318 AC XY: 22171 AN XY: 69796

African (AFR) AF: 0.310 AC: 12027 AN: 38830

American (AMR) AF: 0.214 AC: 2952 AN: 13770

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 836 AN: 3418

East Asian (EAS) AF: 0.0873 AC: 439 AN: 5028

South Asian (SAS) AF: 0.337 AC: 1456 AN: 4320

European-Finnish (FIN) AF: 0.431 AC: 4198 AN: 9740

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 22758 AN: 66478

Other (OTH) AF: 0.311 AC: 604 AN: 1944

Alfa AF: 0.330 Hom.: 13888

Bravo AF: 0.300

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.68
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs4387213; hg19: chr1-17815433;