chr5-52136835-G-T

Variant names:

• chr5-52136835-G-T
• rs4507452
• ENST00000797160.1:n.235-361G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000797160.1(ENSG00000303782):​n.235-361G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,020 control chromosomes in the GnomAD database, including 8,414 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 0.32 (8414 hom., cov: 32)
• Consequence: ENSG00000303782 ENST00000797160.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 0 publications found

Genes affected

ENSG00000303782 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378961	XR_948317.2	n.321-361G>T		intron_variant	Intron 3 of 3
LOC105378961	XR_948318.2	n.218-361G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303782	ENST00000797160.1	n.235-361G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48008 AN: 151902 Hom.: 8406 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.316 AC: 48026 AN: 152020 Hom.: 8414 Cov.: 32 AF XY: 0.318 AC XY: 23615 AN XY: 74322

African (AFR) AF: 0.181 AC: 7526 AN: 41490

American (AMR) AF: 0.371 AC: 5663 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 896 AN: 3466

East Asian (EAS) AF: 0.588 AC: 3035 AN: 5158

South Asian (SAS) AF: 0.399 AC: 1924 AN: 4818

European-Finnish (FIN) AF: 0.349 AC: 3686 AN: 10550

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.358 AC: 24314 AN: 67944

Other (OTH) AF: 0.300 AC: 633 AN: 2110

Alfa AF: 0.342 Hom.: 15356

Bravo AF: 0.314

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.39
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs4507452; hg19: chr5-51432669;