5-159311504-C-T

Position:

• chr5-159311504-C-T

Variant summary

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

The XR_941138.3(LOC105377683):​n.400+90C>T 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 0.586 in 152,038 control chromosomes in the GnomAD database, including 26,539 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 0.59 (26539 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LOC105377683 XR_941138.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594

Genes affected

LOC105377683 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377683	XR_941138.3	n.400+90C>T		intron_variant, non_coding_transcript_variant
LOC105377683	XR_007059021.1	n.490C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000641961.1	n.567C>T		non_coding_transcript_exon_variant	2/2
	ENST00000521472.6	n.289+90C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89086 AN: 151920 Hom.: 26528 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.570

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.586 AC: 89145 AN: 152038 Hom.: 26539 Cov.: 32 AF XY: 0.592 AC XY: 43991 AN XY: 74270

Gnomad4 AFR AF: 0.667

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.569

Alfa AF: 0.523 Hom.: 7482

Bravo AF: 0.594

Asia WGS AF: 0.715 AC: 2487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6870828; hg19: chr5-158738512;