rs11990854

Variant names:

• chr8-49079489-T-C
• rs11990854
• ENST00000779406.1:n.468-1717A>G

Variant summary

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

The ENST00000779406.1(ENSG00000301510):​n.468-1717A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 152,028 control chromosomes in the GnomAD database, including 20,293 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 0.50 (20293 hom., cov: 32)
• Consequence: ENSG00000301510 ENST00000779406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75
• Publications: 1 publications found

Genes affected

ENSG00000301510 (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 (EAS) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301510	ENST00000779406.1	n.468-1717A>G		intron_variant	Intron 2 of 2
ENSG00000301510	ENST00000779407.1	n.671-1717A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76455 AN: 151910 Hom.: 20264 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.503 AC: 76516 AN: 152028 Hom.: 20293 Cov.: 32 AF XY: 0.511 AC XY: 37965 AN XY: 74280

African (AFR) AF: 0.342 AC: 14173 AN: 41476

American (AMR) AF: 0.606 AC: 9258 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3470

East Asian (EAS) AF: 0.823 AC: 4249 AN: 5164

South Asian (SAS) AF: 0.451 AC: 2168 AN: 4812

European-Finnish (FIN) AF: 0.634 AC: 6696 AN: 10566

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36689 AN: 67958

Other (OTH) AF: 0.516 AC: 1088 AN: 2110

Alfa AF: 0.504 Hom.: 2555

Bravo AF: 0.501

Asia WGS AF: 0.596 AC: 2071 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	0.065
DANN	Benign	0.50
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs11990854; hg19: chr8-49992048;