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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786408.1. 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
	ENSG00000302402	ENST00000786408.1		n.238-12456A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10505241;

hg19: chr8-115960532;