2-203740764-C-T

Variant names:

• chr2-203740764-C-T
• rs4673260

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 0.673 in 152,086 control chromosomes in the GnomAD database, including 35,006 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 0.67 (35006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102367 AN: 151968 Hom.: 34997 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.673 AC: 102414 AN: 152086 Hom.: 35006 Cov.: 32 AF XY: 0.675 AC XY: 50172 AN XY: 74340

African (AFR) AF: 0.596 AC: 24724 AN: 41468

American (AMR) AF: 0.652 AC: 9953 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2305 AN: 3468

East Asian (EAS) AF: 0.413 AC: 2133 AN: 5160

South Asian (SAS) AF: 0.835 AC: 4020 AN: 4814

European-Finnish (FIN) AF: 0.766 AC: 8111 AN: 10584

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.720 AC: 48949 AN: 68004

Other (OTH) AF: 0.664 AC: 1403 AN: 2112

Alfa AF: 0.712 Hom.: 17474

Bravo AF: 0.655

Asia WGS AF: 0.658 AC: 2288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.8
DANN	Benign	0.20
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs4673260; hg19: chr2-204605487;