chr8-137868892-C-T

Variant names:

• chr8-137868892-C-T
• rs1877332
• ENST00000518973.1:n.515-31007G>A

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.515-31007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,150 control chromosomes in the GnomAD database, including 58,442 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 0.87 (58442 hom., cov: 32)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• 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=-1.03).
• 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.574-31007G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253288	ENST00000518973.1	TSL:2	n.515-31007G>A		intron	N/A
	ENSG00000254361	ENST00000519652.3	TSL:4	n.314+11773C>T		intron	N/A
	ENSG00000253288	ENST00000657186.1		n.602-31007G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132453 AN: 152032 Hom.: 58390 Cov.: 32

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.931

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.871 AC: 132560 AN: 152150 Hom.: 58442 Cov.: 32 AF XY: 0.874 AC XY: 65013 AN XY: 74382

African (AFR) AF: 0.723 AC: 29960 AN: 41434

American (AMR) AF: 0.910 AC: 13918 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3115 AN: 3472

East Asian (EAS) AF: 0.950 AC: 4909 AN: 5168

South Asian (SAS) AF: 0.924 AC: 4452 AN: 4820

European-Finnish (FIN) AF: 0.936 AC: 9931 AN: 10608

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

European-Non Finnish (NFE) AF: 0.931 AC: 63350 AN: 68038

Other (OTH) AF: 0.875 AC: 1844 AN: 2108

Alfa AF: 0.893 Hom.: 9910

Bravo AF: 0.861

Asia WGS AF: 0.913 AC: 3173 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	0.67
DANN	Benign	0.40
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1877332; hg19: chr8-138881135;