2-85675446-T-C

Variant names:

• chr2-85675446-T-C
• rs1030862

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 0.411 in 152,070 control chromosomes in the GnomAD database, including 13,039 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 0.41 (13039 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156
• Publications: 18 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 = 0.514 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: 0.411 AC: 62453 AN: 151952 Hom.: 13025 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.411 AC: 62502 AN: 152070 Hom.: 13039 Cov.: 32 AF XY: 0.412 AC XY: 30618 AN XY: 74336

African (AFR) AF: 0.439 AC: 18212 AN: 41452

American (AMR) AF: 0.417 AC: 6371 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3472

East Asian (EAS) AF: 0.531 AC: 2744 AN: 5168

South Asian (SAS) AF: 0.474 AC: 2284 AN: 4820

European-Finnish (FIN) AF: 0.324 AC: 3427 AN: 10582

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26245 AN: 67980

Other (OTH) AF: 0.421 AC: 887 AN: 2108

Alfa AF: 0.401 Hom.: 20978

Bravo AF: 0.420

Asia WGS AF: 0.457 AC: 1586 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	1.2
DANN	Benign	0.74
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1030862; hg19: chr2-85902569;