chr1-217353682-C-G

Variant names:

• chr1-217353682-C-G
• rs1497828

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 0.665 in 151,844 control chromosomes in the GnomAD database, including 35,788 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 0.66 (35788 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.665 AC: 100863 AN: 151726 Hom.: 35778 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.665 AC: 100902 AN: 151844 Hom.: 35788 Cov.: 31 AF XY: 0.668 AC XY: 49586 AN XY: 74196

African (AFR) AF: 0.396 AC: 16390 AN: 41380

American (AMR) AF: 0.724 AC: 11039 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2599 AN: 3470

East Asian (EAS) AF: 0.823 AC: 4226 AN: 5136

South Asian (SAS) AF: 0.675 AC: 3238 AN: 4796

European-Finnish (FIN) AF: 0.840 AC: 8860 AN: 10550

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.770 AC: 52306 AN: 67964

Other (OTH) AF: 0.668 AC: 1407 AN: 2106

Alfa AF: 0.748 Hom.: 21463

Bravo AF: 0.647

Asia WGS AF: 0.703 AC: 2445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.69
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1497828; hg19: chr1-217527024; COSMIC: COSV60026198;