rs9461688

Positions:

• chr6-31303939-A-G

Variant summary

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

The XR_926691.3(LOC112267902):​n.965-2085T>C 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 0.338 in 151,874 control chromosomes in the GnomAD database, including 8,934 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 0.34 (8934 hom., cov: 32)
• Consequence: LOC112267902 XR_926691.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112267902	XR_926691.3	n.965-2085T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51249 AN: 151756 Hom.: 8925 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.338 AC: 51292 AN: 151874 Hom.: 8934 Cov.: 32 AF XY: 0.341 AC XY: 25305 AN XY: 74232

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.336

Alfa AF: 0.301 Hom.: 4591

Bravo AF: 0.337

Asia WGS AF: 0.298 AC: 1039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9461688; hg19: chr6-31271716;