2-149031670-C-T

Variant names:

• chr2-149031670-C-T
• rs17347194

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 0.121 in 152,202 control chromosomes in the GnomAD database, including 1,435 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 0.12 (1435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18437 AN: 152084 Hom.: 1431 Cov.: 32

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0843

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.121 AC: 18449 AN: 152202 Hom.: 1435 Cov.: 32 AF XY: 0.121 AC XY: 9024 AN XY: 74400

African (AFR) AF: 0.0312 AC: 1295 AN: 41550

American (AMR) AF: 0.224 AC: 3428 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3472

East Asian (EAS) AF: 0.0845 AC: 437 AN: 5170

South Asian (SAS) AF: 0.135 AC: 649 AN: 4812

European-Finnish (FIN) AF: 0.119 AC: 1255 AN: 10586

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10403 AN: 68006

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.149 Hom.: 3966

Bravo AF: 0.126

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.21
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs17347194; hg19: chr2-149888184;