5-93156259-C-G

Position:

• chr5-93156259-C-G

Variant summary

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

The XR_007058869.1(LOC105379083):​n.120-6353G>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 0.208 in 152,128 control chromosomes in the GnomAD database, including 4,255 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 0.21 (4255 hom., cov: 32)
• Consequence: LOC105379083 XR_007058869.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947

Genes affected

LOC105379083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379083	XR_007058869.1	n.120-6353G>C		intron_variant, non_coding_transcript_variant
LOC105379083	XR_948569.3	n.127+6102G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31605 AN: 152010 Hom.: 4252 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.208 AC: 31600 AN: 152128 Hom.: 4255 Cov.: 32 AF XY: 0.213 AC XY: 15869 AN XY: 74348

Gnomad4 AFR AF: 0.0498

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.221

Alfa AF: 0.140 Hom.: 297

Bravo AF: 0.206

Asia WGS AF: 0.321 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.76
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12522702; hg19: chr5-92491965;