rs199076

Variant names:

• chr6-23472836-A-G
• rs199076
• ENST00000690652.3:n.356-15166T>C

Variant summary

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

The ENST00000690652.3(ENSG00000289368):​n.356-15166T>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 ENST00000690652.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.552
• Publications: 4 publications found

Genes affected

ENSG00000289368 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105374976	XR_001744046.2	n.401-15166T>C		intron_variant	Intron 3 of 6
LOC105374976	XR_007059501.1	n.379-15166T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289368	ENST00000690652.3	n.356-15166T>C		intron_variant	Intron 1 of 2
ENSG00000289368	ENST00000700866.2	n.181-15166T>C		intron_variant	Intron 1 of 2
ENSG00000289368	ENST00000702216.2	n.203-15166T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.213 AC: 8409 AN: 39566

American (AMR) AF: 0.163 AC: 2093 AN: 12858

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 416 AN: 3332

East Asian (EAS) AF: 0.302 AC: 1372 AN: 4546

South Asian (SAS) AF: 0.181 AC: 786 AN: 4342

European-Finnish (FIN) AF: 0.130 AC: 1077 AN: 8286

Middle Eastern (MID) AF: 0.204 AC: 55 AN: 270

European-Non Finnish (NFE) AF: 0.110 AC: 7208 AN: 65352

Other (OTH) AF: 0.166 AC: 320 AN: 1924

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
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs199076; hg19: chr6-23473064;