8-8744686-C-A

Variant names:

• chr8-8744686-C-A
• rs10503393
• ENST00000522213.5:n.624+9314G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522213.5(ENSG00000254367):​n.624+9314G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 150,322 control chromosomes in the GnomAD database, including 236 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 0.047 (236 hom., cov: 31)
• Consequence: ENSG00000254367 ENST00000522213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0797 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
ENSG00000254367	ENST00000522213.5	n.624+9314G>T		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0467 AC: 7022 AN: 150266 Hom.: 236 Cov.: 31

Gnomad AFR AF: 0.0820

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0203

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0253

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0429

Gnomad OTH AF: 0.0404

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

GnomAD4 genome AF: 0.0468 AC: 7032 AN: 150322 Hom.: 236 Cov.: 31 AF XY: 0.0439 AC XY: 3216 AN XY: 73224

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.0202

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0253

Gnomad4 NFE AF: 0.0429

Gnomad4 OTH AF: 0.0401

Alfa AF: 0.0357 Hom.: 138

Bravo AF: 0.0471

Asia WGS AF: 0.00895 AC: 32 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.91
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503393; hg19: chr8-8602196;