1-226413434-T-C

Variant names:

• chr1-226413434-T-C
• rs2249844

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 0.453 in 152,036 control chromosomes in the GnomAD database, including 17,179 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 0.45 (17179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68704 AN: 151916 Hom.: 17144 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.453 AC: 68804 AN: 152036 Hom.: 17179 Cov.: 32 AF XY: 0.456 AC XY: 33926 AN XY: 74320

African (AFR) AF: 0.636 AC: 26366 AN: 41454

American (AMR) AF: 0.466 AC: 7117 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1042 AN: 3470

East Asian (EAS) AF: 0.799 AC: 4139 AN: 5180

South Asian (SAS) AF: 0.376 AC: 1816 AN: 4824

European-Finnish (FIN) AF: 0.428 AC: 4512 AN: 10534

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22655 AN: 67982

Other (OTH) AF: 0.409 AC: 866 AN: 2116

Alfa AF: 0.340 Hom.: 5047

Bravo AF: 0.469

Asia WGS AF: 0.546 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs2249844; hg19: chr1-226601135;