rs9357347

Positions:

• chr6-41182853-A-C
• chr6-41182853-A-T

Variant summary

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

The XR_001744118.2(LOC107986595):​n.466+258T>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 0.242 in 152,048 control chromosomes in the GnomAD database, including 5,299 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 (5299 hom., cov: 32)
• Consequence: LOC107986595 XR_001744118.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

LOC107986595 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986595	XR_001744118.2	n.466+258T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36747 AN: 151930 Hom.: 5296 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.242 AC: 36756 AN: 152048 Hom.: 5299 Cov.: 32 AF XY: 0.245 AC XY: 18233 AN XY: 74310

Gnomad4 AFR AF: 0.0750

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.245

Alfa AF: 0.277 Hom.: 3503

Bravo AF: 0.233

Asia WGS AF: 0.307 AC: 1067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9357347; hg19: chr6-41150591;