chr2-203826815-C-T

Variant names:

• chr2-203826815-C-T
• rs6745050

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 0.345 in 152,028 control chromosomes in the GnomAD database, including 10,030 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 0.35 (10030 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 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: 0.346 AC: 52517 AN: 151910 Hom.: 10031 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.345 AC: 52519 AN: 152028 Hom.: 10030 Cov.: 32 AF XY: 0.345 AC XY: 25610 AN XY: 74322

African (AFR) AF: 0.188 AC: 7790 AN: 41480

American (AMR) AF: 0.396 AC: 6053 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1696 AN: 3462

East Asian (EAS) AF: 0.246 AC: 1269 AN: 5168

South Asian (SAS) AF: 0.592 AC: 2854 AN: 4820

European-Finnish (FIN) AF: 0.308 AC: 3253 AN: 10574

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

European-Non Finnish (NFE) AF: 0.415 AC: 28212 AN: 67936

Other (OTH) AF: 0.408 AC: 859 AN: 2104

Alfa AF: 0.396 Hom.: 3702

Bravo AF: 0.339

Asia WGS AF: 0.439 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6745050; hg19: chr2-204691538;