rs4094394

Positions:

• chr6-54755305-C-T

Variant summary

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

The XR_001744176.3(LOC107986606):​n.95+46432G>A 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 0.245 in 151,724 control chromosomes in the GnomAD database, including 5,227 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 (5227 hom., cov: 32)
• Consequence: LOC107986606 XR_001744176.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433

Genes affected

LOC107986606 (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 = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986606	XR_001744176.3	n.95+46432G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37102 AN: 151606 Hom.: 5214 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.245 AC: 37152 AN: 151724 Hom.: 5227 Cov.: 32 AF XY: 0.251 AC XY: 18617 AN XY: 74120

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.260

Alfa AF: 0.209 Hom.: 504

Bravo AF: 0.260

Asia WGS AF: 0.369 AC: 1275 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4094394; hg19: chr6-54620103;