2-118114851-T-C

Variant names:

• chr2-118114851-T-C
• rs3849327

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 0.246 in 152,130 control chromosomes in the GnomAD database, including 5,945 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 0.25 (5945 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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: 0.246 AC: 37414 AN: 152014 Hom.: 5937 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.246 AC: 37473 AN: 152130 Hom.: 5945 Cov.: 33 AF XY: 0.244 AC XY: 18177 AN XY: 74384

African (AFR) AF: 0.446 AC: 18510 AN: 41466

American (AMR) AF: 0.221 AC: 3374 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3468

East Asian (EAS) AF: 0.0222 AC: 115 AN: 5178

South Asian (SAS) AF: 0.126 AC: 607 AN: 4812

European-Finnish (FIN) AF: 0.195 AC: 2063 AN: 10600

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11362 AN: 68000

Other (OTH) AF: 0.238 AC: 502 AN: 2110

Alfa AF: 0.182 Hom.: 3858

Bravo AF: 0.258

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.41
DANN	Benign	0.46
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3849327; hg19: chr2-118872427; COSMIC: COSV55522229;