ENST00000817238.1:n.201-1022T>C

Variant names:

• chr6-155812754-A-G
• rs10499299
• ENST00000817238.1:n.201-1022T>C

Variant summary

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

The ENST00000817238.1(ENSG00000287092):​n.201-1022T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,130 control chromosomes in the GnomAD database, including 1,509 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 0.14 (1509 hom., cov: 32)
• Consequence: ENSG00000287092 ENST00000817238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 2 publications found

Genes affected

ENSG00000287092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928923	XR_001744423.2	n.699-715T>C		intron_variant	Intron 6 of 8
LOC105378072	XR_001744424.2	n.79+19335A>G		intron_variant	Intron 1 of 2
LOC105378072	XR_007059824.1	n.79+19335A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287092	ENST00000817238.1	n.201-1022T>C		intron_variant	Intron 1 of 2
ENSG00000287092	ENST00000817239.1	n.160-715T>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20514 AN: 152012 Hom.: 1500 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.135 AC: 20554 AN: 152130 Hom.: 1509 Cov.: 32 AF XY: 0.134 AC XY: 9960 AN XY: 74372

African (AFR) AF: 0.147 AC: 6101 AN: 41472

American (AMR) AF: 0.149 AC: 2276 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.0562 AC: 291 AN: 5174

South Asian (SAS) AF: 0.108 AC: 523 AN: 4828

European-Finnish (FIN) AF: 0.136 AC: 1439 AN: 10582

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.132 AC: 8954 AN: 68002

Other (OTH) AF: 0.125 AC: 264 AN: 2110

Alfa AF: 0.136 Hom.: 2826

Bravo AF: 0.139

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.74
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10499299; hg19: chr6-156133888;