10-81806930-C-T

Variant names:

• chr10-81806930-C-T
• rs9787485
• ENST00000821630.1:n.440-12325G>A

Variant summary

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

The ENST00000821630.1(ENSG00000287358):​n.440-12325G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,870 control chromosomes in the GnomAD database, including 2,594 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 0.18 (2594 hom., cov: 31)
• Consequence: ENSG00000287358 ENST00000821630.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 7 publications found

Genes affected

ENSG00000287358 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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
ENSG00000287358	ENST00000821630.1	n.440-12325G>A		intron_variant	Intron 3 of 4
ENSG00000287358	ENST00000821631.1	n.248-12325G>A		intron_variant	Intron 2 of 3
ENSG00000287358	ENST00000821632.1	n.304-12325G>A		intron_variant	Intron 3 of 4
ENSG00000287358	ENST00000821633.1	n.329+10447G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28069 AN: 151752 Hom.: 2589 Cov.: 31

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.185 AC: 28091 AN: 151870 Hom.: 2594 Cov.: 31 AF XY: 0.186 AC XY: 13806 AN XY: 74190

African (AFR) AF: 0.158 AC: 6565 AN: 41440

American (AMR) AF: 0.184 AC: 2804 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1211 AN: 5132

South Asian (SAS) AF: 0.221 AC: 1061 AN: 4808

European-Finnish (FIN) AF: 0.202 AC: 2124 AN: 10508

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.194 AC: 13162 AN: 67958

Other (OTH) AF: 0.178 AC: 375 AN: 2112

Alfa AF: 0.190 Hom.: 4555

Bravo AF: 0.179

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.5
DANN	Benign	0.78
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs9787485; hg19: chr10-83566686;