5-36473135-C-T

Variant names:

• chr5-36473135-C-T
• rs2937550

Variant summary

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

The variant allele was found at a frequency of 0.384 in 151,988 control chromosomes in the GnomAD database, including 12,482 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 0.38 (12482 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

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 = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58392 AN: 151870 Hom.: 12479 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.384 AC: 58414 AN: 151988 Hom.: 12482 Cov.: 33 AF XY: 0.388 AC XY: 28786 AN XY: 74284

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.400

Alfa AF: 0.440 Hom.: 25652

Bravo AF: 0.382

Asia WGS AF: 0.480 AC: 1669 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	1.7
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2937550; hg19: chr5-36473237;