2-218856467-C-T

Variant names:

• chr2-218856467-C-T
• rs11695967

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 0.193 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.192

Alfa AF: 0.190 Hom.: 5006

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11695967; hg19: chr2-219721190;