8-138071534-C-A

Variant names:

• chr8-138071534-C-A
• rs6577869
• ENST00000518973.1:n.514+11523G>T

Variant summary

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

The ENST00000518973.1(ENSG00000253288):​n.514+11523G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,264 control chromosomes in the GnomAD database, including 24,615 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 0.56 (24615 hom., cov: 29)
• Consequence: ENSG00000253288 ENST00000518973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC401478	NR_161374.1	n.489+11523G>T		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253288	ENST00000518973.1	n.514+11523G>T		intron_variant	Intron 1 of 2	2
ENSG00000254361	ENST00000521793.2	n.629-1367C>A		intron_variant	Intron 1 of 1	2
ENSG00000253288	ENST00000657186.1	n.601+11523G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84695 AN: 151152 Hom.: 24596 Cov.: 29

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.560 AC: 84746 AN: 151264 Hom.: 24615 Cov.: 29 AF XY: 0.574 AC XY: 42407 AN XY: 73872

African (AFR) AF: 0.441 AC: 18144 AN: 41140

American (AMR) AF: 0.662 AC: 10070 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2017 AN: 3470

East Asian (EAS) AF: 0.991 AC: 5101 AN: 5146

South Asian (SAS) AF: 0.692 AC: 3336 AN: 4818

European-Finnish (FIN) AF: 0.620 AC: 6411 AN: 10344

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37710 AN: 67844

Other (OTH) AF: 0.594 AC: 1241 AN: 2090

Alfa AF: 0.548 Hom.: 2895

Bravo AF: 0.562

Asia WGS AF: 0.823 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.4
DANN	Benign	0.85
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs6577869; hg19: chr8-139083777;