rs11786194

Variant names:

• chr8-33815493-A-G
• rs11786194
• ENST00000521541.2:n.313+19057A>G

Variant summary

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

The ENST00000521541.2(ENSG00000253642):​n.313+19057A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0732 in 152,294 control chromosomes in the GnomAD database, including 645 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 0.073 (645 hom., cov: 32)
• Consequence: ENSG00000253642 ENST00000521541.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 3 publications found

Genes affected

ENSG00000253642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521541.2. 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
	LOC105379364	NR_189605.1		n.745+19057A>G		intron	N/A
	LOC105379364	NR_189606.1		n.330+19057A>G		intron	N/A
	LOC105379364	NR_189607.1		n.330+19057A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253642	ENST00000521541.2	TSL:2	n.313+19057A>G		intron	N/A
	ENSG00000253642	ENST00000523063.5	TSL:3	n.504+19057A>G		intron	N/A
	ENSG00000253642	ENST00000523336.2	TSL:2	n.147+19057A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0732 AC: 11141 AN: 152176 Hom.: 644 Cov.: 32

Gnomad AFR AF: 0.0196

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0563

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0999

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0907

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0732 AC: 11147 AN: 152294 Hom.: 645 Cov.: 32 AF XY: 0.0752 AC XY: 5605 AN XY: 74486

African (AFR) AF: 0.0196 AC: 814 AN: 41586

American (AMR) AF: 0.0563 AC: 861 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0450 AC: 156 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1335 AN: 5178

South Asian (SAS) AF: 0.109 AC: 527 AN: 4822

European-Finnish (FIN) AF: 0.0999 AC: 1061 AN: 10616

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0907 AC: 6167 AN: 68016

Other (OTH) AF: 0.0710 AC: 150 AN: 2114

Alfa AF: 0.0811 Hom.: 969

Bravo AF: 0.0680

Asia WGS AF: 0.165 AC: 571 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.73
PhyloP100		-0.19

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: rs11786194;

hg19: chr8-33673011;