rs4352696

chr6-142034354-A-G

Variant summary

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

The XR_001744394.2(LOC107986654):n.89+1162A>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 0.653 in 152,144 control chromosomes in the GnomAD database, including 34,552 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 0.65 (34552 hom., cov: 33)
• Consequence: LOC107986654 XR_001744394.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

Genes affected

LOC107986654 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986654	XR_001744394.2	n.89+1162A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99295 AN: 152026 Hom.: 34485 Cov.: 33

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.653 AC: 99425 AN: 152144 Hom.: 34552 Cov.: 33 AF XY: 0.659 AC XY: 49001 AN XY: 74358

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.644

Alfa AF: 0.631 Hom.: 4573

Bravo AF: 0.677

Asia WGS AF: 0.760 AC: 2640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.44
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: rs4352696; hg19: chr6-142355491;