6-17066914-C-T

Variant names:

• chr6-17066914-C-T
• rs13213842
• ENST00000798149.1:n.225+27232G>A

Variant summary

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

The ENST00000798149.1(ENSG00000287359):​n.225+27232G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,968 control chromosomes in the GnomAD database, including 4,301 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 0.23 (4301 hom., cov: 32)
• Consequence: ENSG00000287359 ENST00000798149.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 4 publications found

Genes affected

ENSG00000287359 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901269	XR_007059481.1	n.39-6080G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287359	ENST00000798149.1	n.225+27232G>A		intron_variant	Intron 1 of 1
ENSG00000287359	ENST00000798150.1	n.224+7252G>A		intron_variant	Intron 2 of 2
ENSG00000287359	ENST00000798151.1	n.212-6080G>A		intron_variant	Intron 1 of 1
ENSG00000287359	ENST00000798152.1	n.487-6080G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35240 AN: 151850 Hom.: 4299 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.232 AC: 35245 AN: 151968 Hom.: 4301 Cov.: 32 AF XY: 0.231 AC XY: 17144 AN XY: 74256

African (AFR) AF: 0.174 AC: 7205 AN: 41442

American (AMR) AF: 0.168 AC: 2569 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3462

East Asian (EAS) AF: 0.221 AC: 1138 AN: 5154

South Asian (SAS) AF: 0.215 AC: 1035 AN: 4822

European-Finnish (FIN) AF: 0.314 AC: 3310 AN: 10538

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18459 AN: 67964

Other (OTH) AF: 0.221 AC: 468 AN: 2114

Alfa AF: 0.268 Hom.: 2654

Bravo AF: 0.218

Asia WGS AF: 0.186 AC: 647 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.79
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs13213842; hg19: chr6-17067145;