chr1-221034542-T-G

Variant names:

• chr1-221034542-T-G
• rs10458466

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 0.454 in 151,738 control chromosomes in the GnomAD database, including 16,078 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 (16078 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68840 AN: 151620 Hom.: 16074 Cov.: 30

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.454 AC: 68884 AN: 151738 Hom.: 16078 Cov.: 30 AF XY: 0.457 AC XY: 33914 AN XY: 74136

African (AFR) AF: 0.361 AC: 14916 AN: 41356

American (AMR) AF: 0.450 AC: 6864 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1500 AN: 3466

East Asian (EAS) AF: 0.469 AC: 2408 AN: 5134

South Asian (SAS) AF: 0.337 AC: 1625 AN: 4816

European-Finnish (FIN) AF: 0.587 AC: 6178 AN: 10520

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34076 AN: 67872

Other (OTH) AF: 0.452 AC: 953 AN: 2110

Alfa AF: 0.473 Hom.: 18347

Bravo AF: 0.441

Asia WGS AF: 0.403 AC: 1402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.57
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10458466; hg19: chr1-221207884; COSMIC: COSV50456101;