rs11789399

Positions:

• chr9-118597008-G-A
• chr9-118597008-G-C

Variant summary

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

The XR_930297.2(LOC105376249):​n.32+133C>T 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 0.35 in 151,984 control chromosomes in the GnomAD database, including 12,077 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 0.35 (12077 hom., cov: 32)
• Consequence: LOC105376249 XR_930297.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.43

Genes affected

LOC105376249 (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 (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376249	XR_930297.2	n.32+133C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53191 AN: 151864 Hom.: 12081 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.0126

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.350 AC: 53171 AN: 151984 Hom.: 12077 Cov.: 32 AF XY: 0.345 AC XY: 25596 AN XY: 74286

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.0128

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.390

Alfa AF: 0.453 Hom.: 21529

Bravo AF: 0.327

Asia WGS AF: 0.132 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11789399; hg19: chr9-121359286;