rs8181320

Variant names:

• chr10-113457106-C-T
• rs8181320
• ENST00000775326.1:n.95-648C>T

Variant summary

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

The ENST00000775326.1(ENSG00000300979):​n.95-648C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,802 control chromosomes in the GnomAD database, including 3,415 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 0.19 (3415 hom., cov: 33)
• Consequence: ENSG00000300979 ENST00000775326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 2 publications found

Genes affected

ENSG00000300979 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 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
ENSG00000300979	ENST00000775326.1	n.95-648C>T		intron_variant	Intron 1 of 2
ENSG00000300979	ENST00000775327.1	n.157-648C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29143 AN: 151686 Hom.: 3419 Cov.: 33

Gnomad AFR AF: 0.0650

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.192 AC: 29125 AN: 151802 Hom.: 3415 Cov.: 33 AF XY: 0.190 AC XY: 14135 AN XY: 74236

African (AFR) AF: 0.0646 AC: 2683 AN: 41506

American (AMR) AF: 0.178 AC: 2716 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1021 AN: 3458

East Asian (EAS) AF: 0.266 AC: 1377 AN: 5174

South Asian (SAS) AF: 0.162 AC: 779 AN: 4818

European-Finnish (FIN) AF: 0.229 AC: 2429 AN: 10588

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17348 AN: 67686

Other (OTH) AF: 0.231 AC: 486 AN: 2102

Alfa AF: 0.212 Hom.: 1709

Bravo AF: 0.184

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.70
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs8181320; hg19: chr10-115216865;