2-204251279-T-C

Variant names:

• chr2-204251279-T-C
• rs6726035

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 0.649 in 152,020 control chromosomes in the GnomAD database, including 32,270 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 0.65 (32270 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.714 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: 0.649 AC: 98600 AN: 151902 Hom.: 32235 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.649 AC: 98678 AN: 152020 Hom.: 32270 Cov.: 31 AF XY: 0.651 AC XY: 48408 AN XY: 74336

African (AFR) AF: 0.604 AC: 25018 AN: 41440

American (AMR) AF: 0.607 AC: 9272 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2106 AN: 3470

East Asian (EAS) AF: 0.459 AC: 2365 AN: 5154

South Asian (SAS) AF: 0.734 AC: 3539 AN: 4822

European-Finnish (FIN) AF: 0.767 AC: 8103 AN: 10570

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46147 AN: 67968

Other (OTH) AF: 0.612 AC: 1287 AN: 2104

Alfa AF: 0.666 Hom.: 57340

Bravo AF: 0.632

Asia WGS AF: 0.612 AC: 2128 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs6726035; hg19: chr2-205116002;