2-204251279-T-C

Position:

• chr2-204251279-T-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.204251279T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.612

Alfa AF: 0.668 Hom.: 46025

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6726035; hg19: chr2-205116002;