rs11987758

Positions:

• chr8-2180583-G-A

Variant summary

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

The ENST00000685917.2(ENSG00000289036):​n.102-2416G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,192 control chromosomes in the GnomAD database, including 1,109 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 0.12 (1109 hom., cov: 32)
• Consequence: ENSG00000289036 ENST00000685917.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

ENSG00000289036 (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 (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377781	XR_941356.3	n.108-12352G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289036	ENST00000685917.2	n.102-2416G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18331 AN: 152072 Hom.: 1110 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.120 AC: 18322 AN: 152192 Hom.: 1109 Cov.: 32 AF XY: 0.119 AC XY: 8852 AN XY: 74408

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0801

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.0939

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.132

Alfa AF: 0.121 Hom.: 831

Bravo AF: 0.120

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.4
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11987758; hg19: chr8-2128786;