rs12401697

Variant names:

• chr1-171419131-G-A
• rs12401697

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 0.526 in 151,904 control chromosomes in the GnomAD database, including 21,070 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 0.53 (21070 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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: 0.526 AC: 79783 AN: 151788 Hom.: 21051 Cov.: 31

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.526 AC: 79841 AN: 151904 Hom.: 21070 Cov.: 31 AF XY: 0.526 AC XY: 39036 AN XY: 74226

African (AFR) AF: 0.559 AC: 23156 AN: 41412

American (AMR) AF: 0.525 AC: 8020 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1684 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1837 AN: 5158

South Asian (SAS) AF: 0.552 AC: 2651 AN: 4804

European-Finnish (FIN) AF: 0.542 AC: 5708 AN: 10526

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35046 AN: 67942

Other (OTH) AF: 0.505 AC: 1067 AN: 2112

Alfa AF: 0.523 Hom.: 3363

Bravo AF: 0.523

Asia WGS AF: 0.435 AC: 1510 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.39
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs12401697; hg19: chr1-171388270;