rs10094837

Variant names:

• chr8-134192893-T-C
• rs10094837
• ENST00000661266.1:n.1311-1036A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661266.1(ENSG00000288067):​n.1311-1036A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,194 control chromosomes in the GnomAD database, including 2,534 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 (2534 hom., cov: 32)
• Consequence: ENSG00000288067 ENST00000661266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315

Genes affected

ENSG00000288067 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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
ENSG00000288067	ENST00000661266.1	n.1311-1036A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26787 AN: 152076 Hom.: 2533 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.176 AC: 26795 AN: 152194 Hom.: 2534 Cov.: 32 AF XY: 0.178 AC XY: 13253 AN XY: 74406

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.178

Alfa AF: 0.151 Hom.: 2373

Bravo AF: 0.189

Asia WGS AF: 0.208 AC: 720 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10094837; hg19: chr8-135205136;