rs10504663

Variant names:

• chr8-77956444-A-T
• rs10504663
• ENST00000730975.1:n.383+8737T>A

Variant summary

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

The ENST00000730975.1(ENSG00000295568):​n.383+8737T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,138 control chromosomes in the GnomAD database, including 5,314 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 0.25 (5314 hom., cov: 32)
• Consequence: ENSG00000295568 ENST00000730975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 1 publications found

Genes affected

ENSG00000295568 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 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
ENSG00000295568	ENST00000730975.1	n.383+8737T>A		intron_variant	Intron 2 of 4
ENSG00000295568	ENST00000730976.1	n.333+671T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37826 AN: 152020 Hom.: 5311 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.249 AC: 37839 AN: 152138 Hom.: 5314 Cov.: 32 AF XY: 0.248 AC XY: 18452 AN XY: 74380

African (AFR) AF: 0.130 AC: 5412 AN: 41530

American (AMR) AF: 0.248 AC: 3797 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3472

East Asian (EAS) AF: 0.155 AC: 804 AN: 5178

South Asian (SAS) AF: 0.404 AC: 1952 AN: 4830

European-Finnish (FIN) AF: 0.270 AC: 2859 AN: 10572

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20357 AN: 67966

Other (OTH) AF: 0.270 AC: 568 AN: 2104

Alfa AF: 0.271 Hom.: 737

Bravo AF: 0.239

Asia WGS AF: 0.316 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.52
DANN	Benign	0.81
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10504663; hg19: chr8-78868679;