1-218342968-G-T

Variant names:

• chr1-218342968-G-T
• rs10495098

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 0.472 in 151,856 control chromosomes in the GnomAD database, including 17,922 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 0.47 (17922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 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: 0.472 AC: 71597 AN: 151740 Hom.: 17890 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.472 AC: 71692 AN: 151856 Hom.: 17922 Cov.: 32 AF XY: 0.470 AC XY: 34921 AN XY: 74238

African (AFR) AF: 0.654 AC: 27082 AN: 41392

American (AMR) AF: 0.356 AC: 5437 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3472

East Asian (EAS) AF: 0.376 AC: 1937 AN: 5146

South Asian (SAS) AF: 0.372 AC: 1790 AN: 4818

European-Finnish (FIN) AF: 0.489 AC: 5152 AN: 10540

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.409 AC: 27795 AN: 67924

Other (OTH) AF: 0.407 AC: 859 AN: 2108

Alfa AF: 0.404 Hom.: 8980

Bravo AF: 0.471

Asia WGS AF: 0.377 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.85
DANN	Benign	0.47
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs10495098; hg19: chr1-218516310;