rs11790994

Variant names:

• chr9-95666984-C-G
• rs11790994
• ENST00000422343.1:n.88+16743C>G

Variant summary

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

The ENST00000580326.2(ENSG00000228142):​n.138+16743C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,128 control chromosomes in the GnomAD database, including 1,511 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 0.13 (1511 hom., cov: 32)
• Consequence: ENSG00000228142 ENST00000580326.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

Genes affected

ENSG00000228142 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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
ENSG00000228142	ENST00000422343.1	n.88+16743C>G		intron_variant	Intron 1 of 1	5
ENSG00000228142	ENST00000580326.2	n.138+16743C>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19307 AN: 152010 Hom.: 1503 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.000388

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.127 AC: 19335 AN: 152128 Hom.: 1511 Cov.: 32 AF XY: 0.126 AC XY: 9370 AN XY: 74362

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0980

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.000389

Gnomad4 SAS AF: 0.0495

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.124

Alfa AF: 0.112 Hom.: 121

Bravo AF: 0.128

Asia WGS AF: 0.0330 AC: 119 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11790994; hg19: chr9-98429266;