2-123004966-C-T

Variant names:

• chr2-123004966-C-T
• rs10183521

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 0.363 in 152,002 control chromosomes in the GnomAD database, including 10,902 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 0.36 (10902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.363 AC: 55121 AN: 151886 Hom.: 10897 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.363 AC: 55143 AN: 152002 Hom.: 10902 Cov.: 32 AF XY: 0.360 AC XY: 26750 AN XY: 74304

African (AFR) AF: 0.216 AC: 8957 AN: 41472

American (AMR) AF: 0.365 AC: 5575 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1165 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1768 AN: 5162

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4820

European-Finnish (FIN) AF: 0.466 AC: 4918 AN: 10558

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30700 AN: 67934

Other (OTH) AF: 0.334 AC: 703 AN: 2106

Alfa AF: 0.398 Hom.: 6765

Bravo AF: 0.351

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.43
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs10183521; hg19: chr2-123762542;