2-120329103-T-C

Variant names:

• chr2-120329103-T-C
• rs7593535
• XM_047446882.1:c.141+297T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047446882.1(LOC105373989):​c.141+297T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,026 control chromosomes in the GnomAD database, including 6,032 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 0.27 (6032 hom., cov: 33)
• Consequence: LOC105373989 XM_047446882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 5 publications found

Genes affected

LOC105373989 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41389 AN: 151908 Hom.: 6007 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.273 AC: 41463 AN: 152026 Hom.: 6032 Cov.: 33 AF XY: 0.274 AC XY: 20375 AN XY: 74320

African (AFR) AF: 0.356 AC: 14750 AN: 41464

American (AMR) AF: 0.328 AC: 5014 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2068 AN: 5160

South Asian (SAS) AF: 0.285 AC: 1371 AN: 4806

European-Finnish (FIN) AF: 0.209 AC: 2204 AN: 10568

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14341 AN: 67950

Other (OTH) AF: 0.271 AC: 572 AN: 2110

Alfa AF: 0.237 Hom.: 8446

Bravo AF: 0.283

Asia WGS AF: 0.361 AC: 1257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7593535; hg19: chr2-121086679;