5-73135655-G-C

Position:

• chr5-73135655-G-C

Variant summary

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

The ENST00000508255.1(ENSG00000251599):​n.174-3372C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,166 control chromosomes in the GnomAD database, including 5,708 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 0.27 (5708 hom., cov: 33)
• Consequence: ENSG00000251599 ENST00000508255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124

Genes affected

ENSG00000251599 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379030	NR_134252.1	n.174-3372C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000251599	ENST00000508255.1	n.174-3372C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40721 AN: 152048 Hom.: 5708 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.268 AC: 40736 AN: 152166 Hom.: 5708 Cov.: 33 AF XY: 0.267 AC XY: 19863 AN XY: 74400

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.279

Alfa AF: 0.155 Hom.: 298

Bravo AF: 0.269

Asia WGS AF: 0.309 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17632159; hg19: chr5-72431482;