ENST00000836218.1:n.63T>C

Variant names:

• chr2-120525054-A-G
• rs17050244
• ENST00000836218.1:n.63T>C

Variant summary

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

The ENST00000836218.1(ENSG00000308744):​n.63T>C 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 0.082 in 152,176 control chromosomes in the GnomAD database, including 683 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 0.082 (683 hom., cov: 33)
• Consequence: ENSG00000308744 ENST00000836218.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 9 publications found

Genes affected

ENSG00000308744 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.215 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
ENSG00000308744	ENST00000836218.1	n.63T>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12491 AN: 152058 Hom.: 683 Cov.: 33

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.0673

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0721

Gnomad OTH AF: 0.0778

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

GnomAD4 genome AF: 0.0820 AC: 12484 AN: 152176 Hom.: 683 Cov.: 33 AF XY: 0.0841 AC XY: 6257 AN XY: 74396

African (AFR) AF: 0.0832 AC: 3456 AN: 41520

American (AMR) AF: 0.0519 AC: 793 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1086 AN: 5174

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4818

European-Finnish (FIN) AF: 0.0673 AC: 712 AN: 10586

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0721 AC: 4902 AN: 67994

Other (OTH) AF: 0.0761 AC: 161 AN: 2116

Alfa AF: 0.0755 Hom.: 890

Bravo AF: 0.0767

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.83
DANN	Benign	0.63
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs17050244; hg19: chr2-121282630;