rs10505241

Variant names:

• chr8-114948303-T-C
• rs10505241
• ENST00000786408.1:n.238-12456A>G

Variant summary

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

The ENST00000786408.1(ENSG00000302402):​n.238-12456A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0523 in 152,246 control chromosomes in the GnomAD database, including 265 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 0.052 (265 hom., cov: 32)
• Consequence: ENSG00000302402 ENST00000786408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 0 publications found

Genes affected

ENSG00000302402 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986901	XR_001745735.2	n.207-12456A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302402	ENST00000786408.1	n.238-12456A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7968 AN: 152128 Hom.: 264 Cov.: 32

Gnomad AFR AF: 0.0567

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0528

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0523 AC: 7970 AN: 152246 Hom.: 265 Cov.: 32 AF XY: 0.0535 AC XY: 3986 AN XY: 74442

African (AFR) AF: 0.0567 AC: 2356 AN: 41548

American (AMR) AF: 0.0364 AC: 556 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0528 AC: 183 AN: 3468

East Asian (EAS) AF: 0.122 AC: 634 AN: 5180

South Asian (SAS) AF: 0.146 AC: 704 AN: 4830

European-Finnish (FIN) AF: 0.0246 AC: 261 AN: 10598

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0463 AC: 3149 AN: 68010

Other (OTH) AF: 0.0506 AC: 107 AN: 2114

Alfa AF: 0.0471 Hom.: 30

Bravo AF: 0.0507

Asia WGS AF: 0.147 AC: 509 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.73
DANN	Benign	0.48
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs10505241; hg19: chr8-115960532;