chr17-29376331-C-T

Variant names:

• chr17-29376331-C-T
• rs2138852
• ENST00000819814.1:n.466G>A

Variant summary

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

The ENST00000819814.1(ENSG00000264808):​n.466G>A 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 0.644 in 151,962 control chromosomes in the GnomAD database, including 33,388 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 0.64 (33388 hom., cov: 31)
• Consequence: ENSG00000264808 ENST00000819814.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 43 publications found

Genes affected

ENSG00000264808 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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
ENSG00000264808	ENST00000819814.1	n.466G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000264808	ENST00000819815.1	n.458G>A		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000264808	ENST00000819824.1	n.296G>A		splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97763 AN: 151842 Hom.: 33336 Cov.: 31

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.644 AC: 97867 AN: 151962 Hom.: 33388 Cov.: 31 AF XY: 0.647 AC XY: 48055 AN XY: 74264

African (AFR) AF: 0.858 AC: 35578 AN: 41468

American (AMR) AF: 0.596 AC: 9096 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3468

East Asian (EAS) AF: 0.969 AC: 5013 AN: 5176

South Asian (SAS) AF: 0.642 AC: 3089 AN: 4814

European-Finnish (FIN) AF: 0.552 AC: 5816 AN: 10540

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.523 AC: 35506 AN: 67934

Other (OTH) AF: 0.590 AC: 1241 AN: 2104

Alfa AF: 0.570 Hom.: 80480

Bravo AF: 0.656

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.42
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs2138852; hg19: chr17-27703349;