rs199076

Positions:

• chr6-23472836-A-G

Variant summary

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

The ENST00000690652.2(ENSG00000289368):​n.211-15166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 141,382 control chromosomes in the GnomAD database, including 1,866 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 0.16 (1866 hom., cov: 30)
• Consequence: ENSG00000289368 ENST00000690652.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552

Genes affected

ENSG00000289368 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374976	XR_001744046.2	n.401-15166T>C		intron_variant
LOC105374976	XR_007059501.1	n.379-15166T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289368	ENST00000690652.2	n.211-15166T>C		intron_variant
ENSG00000289368	ENST00000700866.1	n.181-15166T>C		intron_variant
ENSG00000289368	ENST00000702216.1	n.203-15166T>C		intron_variant
ENSG00000289368	ENST00000702386.1	n.200-15166T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.155 AC: 21912 AN: 141380 Hom.: 1862 Cov.: 30

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.198

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.155 AC: 21921 AN: 141382 Hom.: 1866 Cov.: 30 AF XY: 0.157 AC XY: 10722 AN XY: 68424

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.166

Alfa AF: 0.135 Hom.: 187

Bravo AF: 0.157

Asia WGS AF: 0.232 AC: 780 AN: 3352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs199076; hg19: chr6-23473064;