chr2-173432931-C-T

Variant names:

• chr2-173432931-C-T
• rs10497394
• ENST00000741667.1:n.1596C>T

Variant summary

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

The ENST00000741667.1(ENSG00000296758):​n.1596C>T 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 0.231 in 152,006 control chromosomes in the GnomAD database, including 4,486 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 0.23 (4486 hom., cov: 31)
• Consequence: ENSG00000296758 ENST00000741667.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 16 publications found

Genes affected

ENSG00000296758 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 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
ENSG00000296758	ENST00000741667.1	n.1596C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296758	ENST00000741668.1	n.1427C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296758	ENST00000741669.1	n.1707C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35055 AN: 151888 Hom.: 4484 Cov.: 31

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.231 AC: 35066 AN: 152006 Hom.: 4486 Cov.: 31 AF XY: 0.234 AC XY: 17354 AN XY: 74288

African (AFR) AF: 0.118 AC: 4914 AN: 41474

American (AMR) AF: 0.295 AC: 4502 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3468

East Asian (EAS) AF: 0.378 AC: 1952 AN: 5166

South Asian (SAS) AF: 0.204 AC: 982 AN: 4802

European-Finnish (FIN) AF: 0.266 AC: 2801 AN: 10548

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18359 AN: 67954

Other (OTH) AF: 0.227 AC: 480 AN: 2114

Alfa AF: 0.254 Hom.: 14379

Bravo AF: 0.233

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.71
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10497394; hg19: chr2-174297659;