8-5511006-C-G

Variant names:

• chr8-5511006-C-G
• rs10503309
• ENST00000804953.1:n.130+767C>G

Variant summary

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

The ENST00000804953.1(ENSG00000304614):​n.130+767C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,104 control chromosomes in the GnomAD database, including 4,617 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 0.24 (4617 hom., cov: 32)
• Consequence: ENSG00000304614 ENST00000804953.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 1 publications found

Genes affected

ENSG00000304614 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 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
ENSG00000304614	ENST00000804953.1	n.130+767C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35942 AN: 151986 Hom.: 4615 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.236 AC: 35950 AN: 152104 Hom.: 4617 Cov.: 32 AF XY: 0.233 AC XY: 17292 AN XY: 74342

African (AFR) AF: 0.149 AC: 6170 AN: 41492

American (AMR) AF: 0.235 AC: 3579 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1014 AN: 5170

South Asian (SAS) AF: 0.321 AC: 1549 AN: 4822

European-Finnish (FIN) AF: 0.191 AC: 2023 AN: 10576

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19843 AN: 67990

Other (OTH) AF: 0.243 AC: 514 AN: 2116

Alfa AF: 0.259 Hom.: 658

Bravo AF: 0.235

Asia WGS AF: 0.235 AC: 819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.3
DANN	Benign	0.64
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10503309; hg19: chr8-5368528;