rs10739923

chr9-91984009-T-C

Variant summary

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

The XR_930124.1(LOC105376148):n.362+1686A>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 0.532 in 152,076 control chromosomes in the GnomAD database, including 24,667 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 0.53 (24667 hom., cov: 31)
• Consequence: LOC105376148 XR_930124.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

LOC105376148 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376148	XR_930124.1	n.362+1686A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80737 AN: 151956 Hom.: 24617 Cov.: 31

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.532 AC: 80848 AN: 152076 Hom.: 24667 Cov.: 31 AF XY: 0.531 AC XY: 39495 AN XY: 74326

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.495

Alfa AF: 0.423 Hom.: 6906

Bravo AF: 0.558

Asia WGS AF: 0.484 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
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: rs10739923; hg19: chr9-94746291;