2-120418312-C-T

Variant names:

• chr2-120418312-C-T
• rs4456710

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 0.122 in 152,102 control chromosomes in the GnomAD database, including 1,419 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 0.12 (1419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884
• Publications: 2 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 = 0.356 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: 0.122 AC: 18535 AN: 151984 Hom.: 1425 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0887

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.122 AC: 18541 AN: 152102 Hom.: 1419 Cov.: 32 AF XY: 0.124 AC XY: 9216 AN XY: 74356

African (AFR) AF: 0.156 AC: 6461 AN: 41460

American (AMR) AF: 0.108 AC: 1648 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0427 AC: 148 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1908 AN: 5162

South Asian (SAS) AF: 0.161 AC: 773 AN: 4816

European-Finnish (FIN) AF: 0.121 AC: 1280 AN: 10586

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0887 AC: 6032 AN: 67992

Other (OTH) AF: 0.108 AC: 228 AN: 2114

Alfa AF: 0.0960 Hom.: 2717

Bravo AF: 0.124

Asia WGS AF: 0.257 AC: 892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.96
DANN	Benign	0.67
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs4456710; hg19: chr2-121175888;