rs10503766

Variant names:

• chr8-25064915-G-C
• rs10503766
• ENST00000819292.1:n.143-2904G>C

Variant summary

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

The ENST00000819292.1(ENSG00000306541):​n.143-2904G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0439 in 151,188 control chromosomes in the GnomAD database, including 424 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 0.044 (424 hom., cov: 31)
• Consequence: ENSG00000306541 ENST00000819292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 0 publications found

Genes affected

ENSG00000306541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819292.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306541	ENST00000819292.1		n.143-2904G>C		intron	N/A
	ENSG00000306541	ENST00000819293.1		n.200-2904G>C		intron	N/A
	ENSG00000306541	ENST00000819294.1		n.246-2904G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0438 AC: 6623 AN: 151074 Hom.: 424 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0201

Gnomad ASJ AF: 0.00866

Gnomad EAS AF: 0.000389

Gnomad SAS AF: 0.0113

Gnomad FIN AF: 0.00348

Gnomad MID AF: 0.0224

Gnomad NFE AF: 0.00520

Gnomad OTH AF: 0.0360

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

GnomAD4 genome AF: 0.0439 AC: 6630 AN: 151188 Hom.: 424 Cov.: 31 AF XY: 0.0424 AC XY: 3128 AN XY: 73764

African (AFR) AF: 0.140 AC: 5772 AN: 41166

American (AMR) AF: 0.0200 AC: 302 AN: 15082

Ashkenazi Jewish (ASJ) AF: 0.00866 AC: 30 AN: 3464

East Asian (EAS) AF: 0.000390 AC: 2 AN: 5122

South Asian (SAS) AF: 0.0113 AC: 54 AN: 4778

European-Finnish (FIN) AF: 0.00348 AC: 36 AN: 10350

Middle Eastern (MID) AF: 0.0207 AC: 6 AN: 290

European-Non Finnish (NFE) AF: 0.00520 AC: 353 AN: 67922

Other (OTH) AF: 0.0356 AC: 75 AN: 2104

Alfa AF: 0.0255 Hom.: 24

Bravo AF: 0.0495

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10503766; hg19: chr8-24922430;