2-136166123-C-T

Variant names:

• chr2-136166123-C-T
• rs2176716
• ENST00000805101.1:n.685+38673C>T

Variant summary

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

The ENST00000805101.1(ENSG00000304642):​n.685+38673C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,958 control chromosomes in the GnomAD database, including 5,653 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 0.26 (5653 hom., cov: 31)
• Consequence: ENSG00000304642 ENST00000805101.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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.685+38673C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40035 AN: 151840 Hom.: 5644 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.264 AC: 40090 AN: 151958 Hom.: 5653 Cov.: 31 AF XY: 0.270 AC XY: 20020 AN XY: 74260

African (AFR) AF: 0.279 AC: 11541 AN: 41436

American (AMR) AF: 0.316 AC: 4828 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1555 AN: 3472

East Asian (EAS) AF: 0.411 AC: 2124 AN: 5172

South Asian (SAS) AF: 0.311 AC: 1501 AN: 4824

European-Finnish (FIN) AF: 0.227 AC: 2387 AN: 10496

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15102 AN: 67960

Other (OTH) AF: 0.321 AC: 676 AN: 2108

Alfa AF: 0.254 Hom.: 669

Bravo AF: 0.269

Asia WGS AF: 0.380 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2176716; hg19: chr2-136923693;