rs11760067

Variant names:

• chr6-134773134-C-T
• rs11760067
• ENST00000836833.1:n.267+32604G>A

Variant summary

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

The ENST00000836833.1(ENSG00000308852):​n.267+32604G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.074 in 151,786 control chromosomes in the GnomAD database, including 569 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 0.074 (569 hom., cov: 27)
• Consequence: ENSG00000308852 ENST00000836833.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 7 publications found

Genes affected

ENSG00000308852 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928277	XR_001744363.2	n.395+32604G>A		intron_variant	Intron 2 of 3
LOC101928277	XR_001744364.2	n.342+32604G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308852	ENST00000836833.1	n.267+32604G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0741 AC: 11235 AN: 151668 Hom.: 568 Cov.: 27

Gnomad AFR AF: 0.0194

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0468

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0740 AC: 11231 AN: 151786 Hom.: 569 Cov.: 27 AF XY: 0.0720 AC XY: 5340 AN XY: 74190

African (AFR) AF: 0.0194 AC: 801 AN: 41366

American (AMR) AF: 0.0743 AC: 1131 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3470

East Asian (EAS) AF: 0.0471 AC: 243 AN: 5162

South Asian (SAS) AF: 0.102 AC: 487 AN: 4792

European-Finnish (FIN) AF: 0.0719 AC: 757 AN: 10532

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7052 AN: 67926

Other (OTH) AF: 0.0819 AC: 172 AN: 2100

Alfa AF: 0.0781 Hom.: 103

Bravo AF: 0.0712

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.26
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11760067; hg19: chr6-135094272;