chr8-137869317-C-T

Variant names:

• chr8-137869317-C-T
• rs1511849
• ENST00000518973.1:n.515-31432G>A

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.515-31432G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,146 control chromosomes in the GnomAD database, including 59,498 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 (59498 hom., cov: 30)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 2 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518973.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC401478	NR_161374.1		n.574-31432G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253288	ENST00000518973.1	TSL:2	n.515-31432G>A		intron	N/A
	ENSG00000254361	ENST00000519652.3	TSL:4	n.314+12198C>T		intron	N/A
	ENSG00000253288	ENST00000657186.1		n.602-31432G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.881 AC: 133870 AN: 152030 Hom.: 59442 Cov.: 30

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.881 AC: 133981 AN: 152146 Hom.: 59498 Cov.: 30 AF XY: 0.883 AC XY: 65645 AN XY: 74372

African (AFR) AF: 0.755 AC: 31285 AN: 41458

American (AMR) AF: 0.915 AC: 13999 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3123 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4905 AN: 5164

South Asian (SAS) AF: 0.924 AC: 4446 AN: 4812

European-Finnish (FIN) AF: 0.936 AC: 9923 AN: 10596

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.931 AC: 63358 AN: 68032

Other (OTH) AF: 0.881 AC: 1860 AN: 2112

Alfa AF: 0.885 Hom.: 10855

Bravo AF: 0.873

Asia WGS AF: 0.916 AC: 3185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.50
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1511849; hg19: chr8-138881560;