2-218856467-C-T

Variant names:

• chr2-218856467-C-T
• rs11695967

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 0.193 in 152,112 control chromosomes in the GnomAD database, including 3,108 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 0.19 (3108 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.193 AC: 29335 AN: 151994 Hom.: 3098 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.193 AC: 29362 AN: 152112 Hom.: 3108 Cov.: 32 AF XY: 0.194 AC XY: 14401 AN XY: 74362

African (AFR) AF: 0.177 AC: 7333 AN: 41494

American (AMR) AF: 0.185 AC: 2828 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3466

East Asian (EAS) AF: 0.497 AC: 2568 AN: 5168

South Asian (SAS) AF: 0.183 AC: 883 AN: 4822

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10576

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

European-Non Finnish (NFE) AF: 0.186 AC: 12662 AN: 67986

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.190 Hom.: 8438

Bravo AF: 0.196

Asia WGS AF: 0.328 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.57
DANN	Benign	0.80
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs11695967; hg19: chr2-219721190;