rs11790994

chr9-95666984-C-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, non coding transcript 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: ENST00000580326.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000580326.2	n.138+16743C>G		intron_variant, non_coding_transcript_variant		3
	ENST00000422343.1	n.88+16743C>G		intron_variant, non_coding_transcript_variant		5

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;