chr9-134226324-G-A

Position:

• chr9-134226324-G-A

Variant summary

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

The XR_001746583.1(LOC107987039):​n.684-602C>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 0.543 in 152,044 control chromosomes in the GnomAD database, including 23,571 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 0.54 (23571 hom., cov: 32)
• Consequence: LOC107987039 XR_001746583.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.793

Genes affected

LOC107987039 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987039	XR_001746583.1	n.684-602C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82459 AN: 151926 Hom.: 23536 Cov.: 32

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.543 AC: 82537 AN: 152044 Hom.: 23571 Cov.: 32 AF XY: 0.540 AC XY: 40118 AN XY: 74316

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.543

Alfa AF: 0.498 Hom.: 4362

Bravo AF: 0.557

Asia WGS AF: 0.484 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1475718; hg19: chr9-137118170; COSMIC: COSV60405051;