chr2-41173919-T-C

Variant names:

• chr2-41173919-T-C
• rs12990515

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 0.238 in 152,052 control chromosomes in the GnomAD database, including 4,527 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 0.24 (4527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36238 AN: 151932 Hom.: 4530 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.238 AC: 36249 AN: 152052 Hom.: 4527 Cov.: 32 AF XY: 0.236 AC XY: 17555 AN XY: 74310

African (AFR) AF: 0.215 AC: 8918 AN: 41500

American (AMR) AF: 0.186 AC: 2837 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3466

East Asian (EAS) AF: 0.0387 AC: 200 AN: 5172

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4820

European-Finnish (FIN) AF: 0.281 AC: 2968 AN: 10552

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18488 AN: 67964

Other (OTH) AF: 0.213 AC: 449 AN: 2112

Alfa AF: 0.154 Hom.: 394

Bravo AF: 0.227

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.5
DANN	Benign	0.84
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs12990515; hg19: chr2-41401059;