5-163341300-C-T

Position:

• chr5-163341300-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000503504.1(ENSG00000254186):​n.356-84313G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,952 control chromosomes in the GnomAD database, including 12,476 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 0.40 (12476 hom., cov: 32)
• Consequence: ENSG00000254186 ENST00000503504.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377700	XR_001742961.2	n.1236+71019G>A		intron_variant
LOC105377700	XR_001742965.1	n.1236+71019G>A		intron_variant
LOC105377700	XR_002956233.2	n.1236+71019G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254186	ENST00000503504.1	n.356-84313G>A		intron_variant		5
ENSG00000254186	ENST00000646617.1	n.322+84503G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60071 AN: 151830 Hom.: 12479 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.0661

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.395 AC: 60083 AN: 151952 Hom.: 12476 Cov.: 32 AF XY: 0.387 AC XY: 28688 AN XY: 74218

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.0664

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.415

Alfa AF: 0.436 Hom.: 1835

Bravo AF: 0.392

Asia WGS AF: 0.198 AC: 690 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	2.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs744022; hg19: chr5-162768306;