rs716933

chr9-38332793-A-T

Variant summary

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

The XR_001746670.2(LOC107987065):n.302+16369A>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 0.42 in 151,986 control chromosomes in the GnomAD database, including 13,710 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 0.42 (13710 hom., cov: 32)
• Consequence: LOC107987065 XR_001746670.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456

Genes affected

LOC107987065 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987065	XR_001746670.2	n.302+16369A>T		intron_variant, non_coding_transcript_variant
LOC107987065	XR_001746668.2	n.302+16369A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63726 AN: 151868 Hom.: 13702 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.420 AC: 63761 AN: 151986 Hom.: 13710 Cov.: 32 AF XY: 0.419 AC XY: 31100 AN XY: 74280

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.419

Alfa AF: 0.436 Hom.: 1819

Bravo AF: 0.416

Asia WGS AF: 0.400 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.085
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716933; hg19: chr9-38332790; COSMIC: COSV69461047;