chr8-137906702-C-T

Variant names:

• chr8-137906702-C-T
• rs2705293
• ENST00000518973.1:n.515-68817G>A

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.515-68817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,256 control chromosomes in the GnomAD database, including 59,450 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 0.88 (59450 hom., cov: 33)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 8 publications found

Genes affected

ENSG00000253288 (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 = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC401478	NR_161374.1	n.574-68817G>A		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253288	ENST00000518973.1	n.515-68817G>A		intron_variant	Intron 1 of 2	2
ENSG00000254361	ENST00000519652.3	n.315-21979C>T		intron_variant	Intron 2 of 2	4
ENSG00000253288	ENST00000657186.1	n.602-68817G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133784 AN: 152138 Hom.: 59403 Cov.: 33

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.930

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.879 AC: 133886 AN: 152256 Hom.: 59450 Cov.: 33 AF XY: 0.881 AC XY: 65618 AN XY: 74442

African (AFR) AF: 0.745 AC: 30921 AN: 41522

American (AMR) AF: 0.914 AC: 13987 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3125 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4919 AN: 5176

South Asian (SAS) AF: 0.930 AC: 4481 AN: 4820

European-Finnish (FIN) AF: 0.936 AC: 9934 AN: 10608

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63578 AN: 68028

Other (OTH) AF: 0.879 AC: 1860 AN: 2116

Alfa AF: 0.909 Hom.: 141360

Bravo AF: 0.870

Asia WGS AF: 0.914 AC: 3178 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	1.1
DANN	Benign	0.22
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2705293; hg19: chr8-138918945;