rs10503393

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-8744686-C-A
• chr8-8744686-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000254367	ENST00000765578.1	n.455+12490G>T		intron_variant	Intron 2 of 3
ENSG00000254367	ENST00000765579.1	n.406+12490G>T		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.0820 AC: 3354 AN: 40880

American (AMR) AF: 0.0202 AC: 306 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3466

East Asian (EAS) AF: 0.000196 AC: 1 AN: 5096

South Asian (SAS) AF: 0.0120 AC: 57 AN: 4740

European-Finnish (FIN) AF: 0.0253 AC: 252 AN: 9980

Middle Eastern (MID) AF: 0.0379 AC: 11 AN: 290

European-Non Finnish (NFE) AF: 0.0429 AC: 2910 AN: 67768

Other (OTH) AF: 0.0401 AC: 83 AN: 2070

Alfa AF: 0.0376 Hom.: 186

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
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10503393; hg19: chr8-8602196;