rs9468937

chr6-31302341-C-Achr6-31302341-C-G

Variant summary

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

The XR_926691.3(LOC112267902):n.965-487G>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 0.512 in 151,002 control chromosomes in the GnomAD database, including 20,576 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 0.51 (20576 hom., cov: 29)
• Consequence: LOC112267902 XR_926691.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.965-487G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77264 AN: 150884 Hom.: 20559 Cov.: 29

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.512 AC: 77323 AN: 151002 Hom.: 20576 Cov.: 29 AF XY: 0.516 AC XY: 38100 AN XY: 73774

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.535

Alfa AF: 0.303 Hom.: 695

Bravo AF: 0.513

Asia WGS AF: 0.511 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.18
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9468937; hg19: chr6-31270118;