10-8511107-C-T

Variant names:

• chr10-8511107-C-T
• rs6602318
• ENST00000803407.1:n.539+2803G>A

Variant summary

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

The ENST00000803407.1(ENSG00000304440):​n.539+2803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,080 control chromosomes in the GnomAD database, including 18,328 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 0.49 (18328 hom., cov: 33)
• Consequence: ENSG00000304440 ENST00000803407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 1 publications found

Genes affected

ENSG00000304440 (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 (AMR) allele frequency at 95% confidence interval = 0.497 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
ENSG00000304440	ENST00000803407.1	n.539+2803G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74329 AN: 151962 Hom.: 18322 Cov.: 33

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.489 AC: 74371 AN: 152080 Hom.: 18328 Cov.: 33 AF XY: 0.485 AC XY: 36085 AN XY: 74330

African (AFR) AF: 0.498 AC: 20674 AN: 41476

American (AMR) AF: 0.506 AC: 7747 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1632 AN: 3470

East Asian (EAS) AF: 0.335 AC: 1732 AN: 5174

South Asian (SAS) AF: 0.409 AC: 1970 AN: 4822

European-Finnish (FIN) AF: 0.478 AC: 5041 AN: 10552

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.501 AC: 34048 AN: 67976

Other (OTH) AF: 0.469 AC: 990 AN: 2112

Alfa AF: 0.493 Hom.: 9851

Bravo AF: 0.495

Asia WGS AF: 0.402 AC: 1399 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	0.14
DANN	Benign	0.55
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs6602318; hg19: chr10-8553070;