9-32717015-T-C

Variant summary

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

The XR_929559.2(LOC105376017):n.617-11644A>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 0.583 in 151,952 control chromosomes in the GnomAD database, including 26,352 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 0.58 (26352 hom., cov: 31)
• Consequence: LOC105376017 XR_929559.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

LOC105376017 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376017	XR_929559.2	n.617-11644A>G		intron_variant, non_coding_transcript_variant
LOC105376017	XR_007061451.1	n.617-11644A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88501 AN: 151834 Hom.: 26325 Cov.: 31

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.583 AC: 88572 AN: 151952 Hom.: 26352 Cov.: 31 AF XY: 0.575 AC XY: 42713 AN XY: 74256

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.566

Alfa AF: 0.563 Hom.: 44993

Bravo AF: 0.588

Asia WGS AF: 0.454 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	10
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328994; hg19: chr9-32717013;