chr1-203210156-T-C

Variant names:

• chr1-203210156-T-C
• rs2486953

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 0.493 in 151,986 control chromosomes in the GnomAD database, including 19,595 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 0.49 (19595 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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: 0.493 AC: 74922 AN: 151868 Hom.: 19574 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.493 AC: 74986 AN: 151986 Hom.: 19595 Cov.: 32 AF XY: 0.504 AC XY: 37476 AN XY: 74286

African (AFR) AF: 0.388 AC: 16078 AN: 41438

American (AMR) AF: 0.614 AC: 9387 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1782 AN: 3466

East Asian (EAS) AF: 0.961 AC: 4976 AN: 5180

South Asian (SAS) AF: 0.715 AC: 3453 AN: 4828

European-Finnish (FIN) AF: 0.490 AC: 5171 AN: 10544

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.480 AC: 32601 AN: 67938

Other (OTH) AF: 0.523 AC: 1103 AN: 2110

Alfa AF: 0.487 Hom.: 3705

Bravo AF: 0.495

Asia WGS AF: 0.805 AC: 2795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.079
DANN	Benign	0.40
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2486953; hg19: chr1-203179284;