rs13213842

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798149.1. 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
	ENSG00000287359	ENST00000798149.1		n.225+27232G>A		intron	N/A
	ENSG00000287359	ENST00000798150.1		n.224+7252G>A		intron	N/A
	ENSG00000287359	ENST00000798151.1		n.212-6080G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs13213842;

hg19: chr6-17067145;