chr5-152351716-G-T

Position:

• chr5-152351716-G-T

Variant summary

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

The XR_944433.2(LOC105378237):​n.197+13853G>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 0.334 in 152,052 control chromosomes in the GnomAD database, including 9,187 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 0.33 (9187 hom., cov: 32)
• Consequence: LOC105378237 XR_944433.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

Genes affected

LOC105378237 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378237	XR_944433.2	n.197+13853G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50707 AN: 151936 Hom.: 9167 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.334 AC: 50770 AN: 152052 Hom.: 9187 Cov.: 32 AF XY: 0.333 AC XY: 24715 AN XY: 74320

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.332

Alfa AF: 0.277 Hom.: 10347

Bravo AF: 0.348

Asia WGS AF: 0.318 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	17
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17113138; hg19: chr5-151731277;