5-36473135-C-T

Variant names:

• chr5-36473135-C-T
• rs2937550

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.192 AC: 7945 AN: 41488

American (AMR) AF: 0.476 AC: 7258 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1586 AN: 3464

East Asian (EAS) AF: 0.598 AC: 3081 AN: 5148

South Asian (SAS) AF: 0.402 AC: 1934 AN: 4816

European-Finnish (FIN) AF: 0.447 AC: 4730 AN: 10580

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30581 AN: 67920

Other (OTH) AF: 0.400 AC: 845 AN: 2112

Alfa AF: 0.432 Hom.: 58497

Bravo AF: 0.382

Asia WGS AF: 0.480 AC: 1669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2937550; hg19: chr5-36473237;