chr2-221212505-C-T

Variant names:

• chr2-221212505-C-T
• rs2015298

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 0.909 in 152,260 control chromosomes in the GnomAD database, including 63,673 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 0.91 (63673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 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: 0.909 AC: 138280 AN: 152142 Hom.: 63658 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.909 AC: 138345 AN: 152260 Hom.: 63673 Cov.: 32 AF XY: 0.909 AC XY: 67703 AN XY: 74454

African (AFR) AF: 0.747 AC: 31011 AN: 41512

American (AMR) AF: 0.952 AC: 14562 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3349 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4281 AN: 5176

South Asian (SAS) AF: 0.913 AC: 4401 AN: 4818

European-Finnish (FIN) AF: 0.987 AC: 10484 AN: 10618

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67132 AN: 68046

Other (OTH) AF: 0.916 AC: 1934 AN: 2112

Alfa AF: 0.959 Hom.: 98105

Bravo AF: 0.899

Asia WGS AF: 0.861 AC: 2995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.69
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs2015298; hg19: chr2-222077225;