chr1-111286873-G-T

Variant names:

• chr1-111286873-G-T
• rs12401737

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 0.413 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.249 AC: 10323 AN: 41404

American (AMR) AF: 0.597 AC: 9114 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3470

East Asian (EAS) AF: 0.691 AC: 3552 AN: 5140

South Asian (SAS) AF: 0.429 AC: 2061 AN: 4804

European-Finnish (FIN) AF: 0.431 AC: 4534 AN: 10530

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30106 AN: 67942

Other (OTH) AF: 0.442 AC: 931 AN: 2106

Alfa AF: 0.420 Hom.: 7594

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs12401737; hg19: chr1-111829495;