1-236649839-T-G

Variant names:

• chr1-236649839-T-G
• rs12030126

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 0.485 in 151,942 control chromosomes in the GnomAD database, including 20,960 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 0.48 (20960 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 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: 0.485 AC: 73641 AN: 151824 Hom.: 20960 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.485 AC: 73653 AN: 151942 Hom.: 20960 Cov.: 31 AF XY: 0.483 AC XY: 35871 AN XY: 74266

African (AFR) AF: 0.185 AC: 7681 AN: 41452

American (AMR) AF: 0.477 AC: 7264 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1728 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2449 AN: 5160

South Asian (SAS) AF: 0.423 AC: 2034 AN: 4808

European-Finnish (FIN) AF: 0.674 AC: 7111 AN: 10554

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43828 AN: 67946

Other (OTH) AF: 0.480 AC: 1012 AN: 2108

Alfa AF: 0.567 Hom.: 16980

Bravo AF: 0.450

Asia WGS AF: 0.420 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.2
DANN	Benign	0.82
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs12030126; hg19: chr1-236813139;