2-102263004-C-A

Variant names:

• chr2-102263004-C-A
• rs10189629
• ENST00000804381.1:n.235C>A

Variant summary

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

The ENST00000804381.1(ENSG00000304533):​n.235C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,064 control chromosomes in the GnomAD database, including 1,803 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 0.15 (1803 hom., cov: 32)
• Consequence: ENSG00000304533 ENST00000804381.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 31 publications found

Genes affected

ENSG00000304533 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304533	ENST00000804381.1	n.235C>A		non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22816 AN: 151946 Hom.: 1803 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0757

Gnomad SAS AF: 0.0723

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.150 AC: 22838 AN: 152064 Hom.: 1803 Cov.: 32 AF XY: 0.149 AC XY: 11061 AN XY: 74326

African (AFR) AF: 0.187 AC: 7770 AN: 41478

American (AMR) AF: 0.121 AC: 1847 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 726 AN: 3470

East Asian (EAS) AF: 0.0759 AC: 392 AN: 5166

South Asian (SAS) AF: 0.0724 AC: 349 AN: 4820

European-Finnish (FIN) AF: 0.180 AC: 1902 AN: 10570

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9385 AN: 67966

Other (OTH) AF: 0.153 AC: 323 AN: 2110

Alfa AF: 0.139 Hom.: 6142

Bravo AF: 0.147

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.13
DANN	Benign	0.71
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10189629; hg19: chr2-102879464; COSMIC: COSV60085811;