chr2-155870662-T-C

Variant names:

• chr2-155870662-T-C
• rs13020355
• ENST00000799383.1:n.876+35698A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000799383.1(ENSG00000304068):​n.876+35698A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,154 control chromosomes in the GnomAD database, including 1,328 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 0.12 (1328 hom., cov: 32)
• Consequence: ENSG00000304068 ENST00000799383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.71
• Publications: 2 publications found

Genes affected

ENSG00000304068 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373703	XR_001739749.2	n.638-29678A>G		intron_variant	Intron 4 of 7
LOC105373703	XR_001739750.2	n.638-29678A>G		intron_variant	Intron 4 of 5
LOC105373703	XR_001739751.2	n.638-29678A>G		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304068	ENST00000799383.1	n.876+35698A>G		intron_variant	Intron 6 of 8
ENSG00000304068	ENST00000799384.1	n.693+35698A>G		intron_variant	Intron 1 of 4
ENSG00000304068	ENST00000799387.1	n.118-3475A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18440 AN: 152036 Hom.: 1324 Cov.: 32

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.121 AC: 18448 AN: 152154 Hom.: 1328 Cov.: 32 AF XY: 0.123 AC XY: 9141 AN XY: 74400

African (AFR) AF: 0.0663 AC: 2753 AN: 41544

American (AMR) AF: 0.117 AC: 1792 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 479 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1286 AN: 5176

South Asian (SAS) AF: 0.172 AC: 828 AN: 4826

European-Finnish (FIN) AF: 0.122 AC: 1294 AN: 10596

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9602 AN: 67962

Other (OTH) AF: 0.136 AC: 288 AN: 2110

Alfa AF: 0.132 Hom.: 1351

Bravo AF: 0.116

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	19
DANN	Benign	0.87
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs13020355; hg19: chr2-156727174;