chr1-111286873-G-T

Variant names:

• chr1-111286873-G-T
• rs12401737

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 0.413 in 151,856 control chromosomes in the GnomAD database, including 14,161 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 0.41 (14161 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 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: 0.413 AC: 62620 AN: 151736 Hom.: 14152 Cov.: 31

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.413 AC: 62650 AN: 151856 Hom.: 14161 Cov.: 31 AF XY: 0.416 AC XY: 30882 AN XY: 74222

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.442

Alfa AF: 0.419 Hom.: 6806

Bravo AF: 0.425

Asia WGS AF: 0.527 AC: 1829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.9
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12401737; hg19: chr1-111829495;