chr8-81515555-C-T

Variant names:

• chr8-81515555-C-T
• rs10504740
• ENST00000524085.2:n.435-6152C>T

Variant summary

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

The ENST00000524085.2(ENSG00000253374):​n.435-6152C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,094 control chromosomes in the GnomAD database, including 4,980 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 (4980 hom., cov: 33)
• Consequence: ENSG00000253374 ENST00000524085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 6 publications found

Genes affected

ENSG00000253374 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927118	XR_001745980.2	n.518-10288C>T		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253374	ENST00000524085.2	n.435-6152C>T		intron_variant	Intron 3 of 3	5
ENSG00000253374	ENST00000832857.1	n.327-6152C>T		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832858.1	n.309-6152C>T		intron_variant	Intron 2 of 9
ENSG00000253374	ENST00000832859.1	n.328-6152C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22975 AN: 151976 Hom.: 4953 Cov.: 33

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.0566

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.00727

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.00974

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.152 AC: 23060 AN: 152094 Hom.: 4980 Cov.: 33 AF XY: 0.147 AC XY: 10909 AN XY: 74372

African (AFR) AF: 0.482 AC: 19961 AN: 41432

American (AMR) AF: 0.105 AC: 1605 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3468

East Asian (EAS) AF: 0.0565 AC: 293 AN: 5184

South Asian (SAS) AF: 0.0298 AC: 144 AN: 4826

European-Finnish (FIN) AF: 0.00727 AC: 77 AN: 10592

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.00975 AC: 663 AN: 67984

Other (OTH) AF: 0.126 AC: 266 AN: 2112

Alfa AF: 0.0595 Hom.: 3883

Bravo AF: 0.175

Asia WGS AF: 0.0960 AC: 334 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	0.46
DANN	Benign	0.35
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10504740; hg19: chr8-82427790;