rs9385707

Positions:

• chr6-134847336-T-C

Variant summary

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

The XR_001744364.2(LOC101928277):​n.286+27759A>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 0.235 in 152,148 control chromosomes in the GnomAD database, including 4,619 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 0.24 (4619 hom., cov: 33)
• Consequence: LOC101928277 XR_001744364.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

LOC101928277 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928277	XR_001744364.2	n.286+27759A>G		intron_variant, non_coding_transcript_variant
LOC101928277	XR_001744363.2	n.339+27759A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35759 AN: 152030 Hom.: 4611 Cov.: 33

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.235 AC: 35787 AN: 152148 Hom.: 4619 Cov.: 33 AF XY: 0.244 AC XY: 18137 AN XY: 74396

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.212

Alfa AF: 0.238 Hom.: 5798

Bravo AF: 0.222

Asia WGS AF: 0.204 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.78
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9385707; hg19: chr6-135168474;