rs10491524

Positions:

• chr9-119494976-T-C

Variant summary

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

The XR_930305.2(LOC105376250):​n.188+28919A>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 0.647 in 152,104 control chromosomes in the GnomAD database, including 33,037 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 0.65 (33037 hom., cov: 32)
• Consequence: LOC105376250 XR_930305.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

Genes affected

LOC105376250 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376250	XR_930305.2	n.188+28919A>G		intron_variant, non_coding_transcript_variant
LOC105376250	XR_930304.2	n.188+28919A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98378 AN: 151986 Hom.: 33012 Cov.: 32

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.0982

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.647 AC: 98440 AN: 152104 Hom.: 33037 Cov.: 32 AF XY: 0.640 AC XY: 47578 AN XY: 74350

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.0986

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.701

Gnomad4 OTH AF: 0.639

Alfa AF: 0.677 Hom.: 34548

Bravo AF: 0.637

Asia WGS AF: 0.292 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491524; hg19: chr9-122257254;