rs10504739

chr8-81514819-A-C

Variant summary

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

The ENST00000524085.2(ENSG00000253859):n.435-6888A>C 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 0.153 in 152,138 control chromosomes in the GnomAD database, including 5,074 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 0.15 (5074 hom., cov: 32)
• Consequence: ENST00000524085.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927118	XR_001745980.2	n.518-11024A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000524085.2	n.435-6888A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23144 AN: 152020 Hom.: 5043 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.0301

Gnomad FIN AF: 0.00725

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00970

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.153 AC: 23235 AN: 152138 Hom.: 5074 Cov.: 32 AF XY: 0.148 AC XY: 10987 AN XY: 74398

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.00980

Gnomad4 EAS AF: 0.0565

Gnomad4 SAS AF: 0.0299

Gnomad4 FIN AF: 0.00725

Gnomad4 NFE AF: 0.00972

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0904 Hom.: 688

Bravo AF: 0.176

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504739; hg19: chr8-82427054;