2-85582866-C-T

Variant names:

• chr2-85582866-C-T
• rs1561198

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 0.514 in 152,076 control chromosomes in the GnomAD database, including 21,120 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 0.51 (21120 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 83 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.513 AC: 78027 AN: 151958 Hom.: 21083 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.514 AC: 78119 AN: 152076 Hom.: 21120 Cov.: 32 AF XY: 0.509 AC XY: 37857 AN XY: 74328

African (AFR) AF: 0.691 AC: 28658 AN: 41476

American (AMR) AF: 0.418 AC: 6389 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1390 AN: 3468

East Asian (EAS) AF: 0.392 AC: 2033 AN: 5180

South Asian (SAS) AF: 0.391 AC: 1884 AN: 4822

European-Finnish (FIN) AF: 0.457 AC: 4833 AN: 10580

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31327 AN: 67964

Other (OTH) AF: 0.498 AC: 1052 AN: 2112

Alfa AF: 0.467 Hom.: 56902

Bravo AF: 0.518

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.50
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs1561198; hg19: chr2-85809989;