rs10491790

Positions:

• chr9-79465334-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007061902.1(LOC124902328):​n.84-5332C>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 0.14 in 152,144 control chromosomes in the GnomAD database, including 3,506 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 0.14 (3506 hom., cov: 32)
• Consequence: LOC124902328 XR_007061902.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

Genes affected

LOC124902328 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902328	XR_007061902.1	n.84-5332C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21276 AN: 152026 Hom.: 3499 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.00694

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0447

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.140 AC: 21314 AN: 152144 Hom.: 3506 Cov.: 32 AF XY: 0.135 AC XY: 10016 AN XY: 74398

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.0803

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.00637

Gnomad4 SAS AF: 0.0170

Gnomad4 FIN AF: 0.0171

Gnomad4 NFE AF: 0.0447

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0558 Hom.: 971

Bravo AF: 0.157

Asia WGS AF: 0.0460 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	21
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491790; hg19: chr9-82080249;