chr11-118692090-C-A

Variant names:

• chr11-118692090-C-A
• rs582630
• ENST00000789004.1:n.412-862C>A

Variant summary

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

The ENST00000789004.1(ENSG00000302703):​n.412-862C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,168 control chromosomes in the GnomAD database, including 8,124 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 0.32 (8124 hom., cov: 32)
• Consequence: ENSG00000302703 ENST00000789004.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 9 publications found

Genes affected

ENSG00000302703 (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 (AMR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369519	XR_007062909.1	n.88-862C>A		intron_variant	Intron 1 of 3
LOC105369519	XR_007062910.1	n.42-862C>A		intron_variant	Intron 1 of 3
LOC105369519	XR_948068.3	n.-47C>A		upstream_gene_variant
LOC105369519	XR_948069.3	n.-43C>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302703	ENST00000789004.1	n.412-862C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48423 AN: 152050 Hom.: 8110 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.318 AC: 48455 AN: 152168 Hom.: 8124 Cov.: 32 AF XY: 0.319 AC XY: 23707 AN XY: 74394

African (AFR) AF: 0.250 AC: 10370 AN: 41526

American (AMR) AF: 0.460 AC: 7027 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2098 AN: 5168

South Asian (SAS) AF: 0.189 AC: 913 AN: 4826

European-Finnish (FIN) AF: 0.312 AC: 3303 AN: 10590

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22236 AN: 67978

Other (OTH) AF: 0.333 AC: 703 AN: 2114

Alfa AF: 0.195 Hom.: 438

Bravo AF: 0.334

Asia WGS AF: 0.270 AC: 943 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	1.1
DANN	Benign	0.66
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs582630; hg19: chr11-118562799;