2-221207458-T-C

Variant names:

• chr2-221207458-T-C
• rs17348202

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 0.0465 in 151,772 control chromosomes in the GnomAD database, including 207 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 0.046 (207 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 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: 0.0465 AC: 7055 AN: 151664 Hom.: 206 Cov.: 31

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.0574

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0590

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

GnomAD4 genome AF: 0.0465 AC: 7057 AN: 151772 Hom.: 207 Cov.: 31 AF XY: 0.0464 AC XY: 3440 AN XY: 74118

African (AFR) AF: 0.0210 AC: 872 AN: 41426

American (AMR) AF: 0.0431 AC: 656 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5158

South Asian (SAS) AF: 0.120 AC: 568 AN: 4752

European-Finnish (FIN) AF: 0.0296 AC: 310 AN: 10484

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.0596 AC: 4051 AN: 67942

Other (OTH) AF: 0.0585 AC: 123 AN: 2104

Alfa AF: 0.0605 Hom.: 347

Bravo AF: 0.0452

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.36
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs17348202; hg19: chr2-222072178;