rs1873201

Variant names:

• chr2-163062630-G-A
• rs1873201

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 0.336 in 151,718 control chromosomes in the GnomAD database, including 8,916 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 0.34 (8916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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: 0.336 AC: 50967 AN: 151600 Hom.: 8883 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.336 AC: 51048 AN: 151718 Hom.: 8916 Cov.: 32 AF XY: 0.342 AC XY: 25330 AN XY: 74120

African (AFR) AF: 0.432 AC: 17863 AN: 41378

American (AMR) AF: 0.361 AC: 5488 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3468

East Asian (EAS) AF: 0.438 AC: 2252 AN: 5138

South Asian (SAS) AF: 0.306 AC: 1469 AN: 4806

European-Finnish (FIN) AF: 0.341 AC: 3587 AN: 10528

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.273 AC: 18506 AN: 67878

Other (OTH) AF: 0.342 AC: 719 AN: 2104

Alfa AF: 0.311 Hom.: 996

Bravo AF: 0.342

Asia WGS AF: 0.407 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.32
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1873201; hg19: chr2-163919140;