2-136187459-C-T

Variant names:

• chr2-136187459-C-T
• rs1123848
• ENST00000805101.1:n.686-41516C>T

Variant summary

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

The ENST00000805101.1(ENSG00000304642):​n.686-41516C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,120 control chromosomes in the GnomAD database, including 16,702 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 0.44 (16702 hom., cov: 33)
• Consequence: ENSG00000304642 ENST00000805101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555
• Publications: 6 publications found

Genes affected

ENSG00000304642 (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 = 0.762 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
ENSG00000304642	ENST00000805101.1	n.686-41516C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67236 AN: 152002 Hom.: 16662 Cov.: 33

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.443 AC: 67337 AN: 152120 Hom.: 16702 Cov.: 33 AF XY: 0.452 AC XY: 33605 AN XY: 74372

African (AFR) AF: 0.537 AC: 22289 AN: 41480

American (AMR) AF: 0.597 AC: 9135 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2456 AN: 3470

East Asian (EAS) AF: 0.782 AC: 4052 AN: 5182

South Asian (SAS) AF: 0.529 AC: 2554 AN: 4826

European-Finnish (FIN) AF: 0.331 AC: 3504 AN: 10578

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21753 AN: 67966

Other (OTH) AF: 0.524 AC: 1108 AN: 2116

Alfa AF: 0.375 Hom.: 6050

Bravo AF: 0.466

Asia WGS AF: 0.695 AC: 2417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.35
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1123848; hg19: chr2-136945029;