chr2-102403325-T-C

Variant names:

• chr2-102403325-T-C
• rs1035129

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 0.535 in 151,798 control chromosomes in the GnomAD database, including 23,585 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 0.53 (23585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 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: 0.535 AC: 81107 AN: 151680 Hom.: 23553 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.535 AC: 81192 AN: 151798 Hom.: 23585 Cov.: 32 AF XY: 0.529 AC XY: 39219 AN XY: 74184

African (AFR) AF: 0.733 AC: 30360 AN: 41442

American (AMR) AF: 0.414 AC: 6320 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3470

East Asian (EAS) AF: 0.150 AC: 776 AN: 5174

South Asian (SAS) AF: 0.265 AC: 1277 AN: 4822

European-Finnish (FIN) AF: 0.542 AC: 5724 AN: 10562

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 32919 AN: 67760

Other (OTH) AF: 0.521 AC: 1098 AN: 2106

Alfa AF: 0.519 Hom.: 2771

Bravo AF: 0.536

Asia WGS AF: 0.233 AC: 810 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	0.56
DANN	Benign	0.42
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs1035129; hg19: chr2-103019785;