rs10503393

Positions:

• chr8-8744686-C-A
• chr8-8744686-C-G

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, non coding transcript 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: ENST00000522213.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000522213.5	n.624+9314G>T		intron_variant, non_coding_transcript_variant		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;