6-155812936-C-T

Variant names:

• chr6-155812936-C-T
• rs10499298
• ENST00000817238.1:n.201-1204G>A

Variant summary

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

The ENST00000817238.1(ENSG00000287092):​n.201-1204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,002 control chromosomes in the GnomAD database, including 1,229 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 0.12 (1229 hom., cov: 31)
• Consequence: ENSG00000287092 ENST00000817238.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000817238.1. 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
	ENSG00000287092	ENST00000817238.1		n.201-1204G>A		intron	N/A
	ENSG00000287092	ENST00000817239.1		n.160-897G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18623 AN: 151884 Hom.: 1225 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.123 AC: 18649 AN: 152002 Hom.: 1229 Cov.: 31 AF XY: 0.122 AC XY: 9040 AN XY: 74288

African (AFR) AF: 0.109 AC: 4534 AN: 41438

American (AMR) AF: 0.140 AC: 2131 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3466

East Asian (EAS) AF: 0.0555 AC: 287 AN: 5172

South Asian (SAS) AF: 0.102 AC: 491 AN: 4816

European-Finnish (FIN) AF: 0.136 AC: 1438 AN: 10552

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8820 AN: 67976

Other (OTH) AF: 0.116 AC: 245 AN: 2108

Alfa AF: 0.127 Hom.: 685

Bravo AF: 0.125

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.78
DANN	Benign	0.45
PhyloP100		-0.70

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: rs10499298;

hg19: chr6-156134070;