5-36367758-C-T

Variant names:

• chr5-36367758-C-T
• rs4354072

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 0.336 in 152,088 control chromosomes in the GnomAD database, including 8,754 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 0.34 (8754 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 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: 0.336 AC: 51069 AN: 151966 Hom.: 8736 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.336 AC: 51140 AN: 152088 Hom.: 8754 Cov.: 33 AF XY: 0.338 AC XY: 25158 AN XY: 74352

African (AFR) AF: 0.361 AC: 14958 AN: 41482

American (AMR) AF: 0.278 AC: 4251 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1767 AN: 5156

South Asian (SAS) AF: 0.440 AC: 2122 AN: 4818

European-Finnish (FIN) AF: 0.360 AC: 3811 AN: 10572

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22267 AN: 67982

Other (OTH) AF: 0.333 AC: 703 AN: 2114

Alfa AF: 0.328 Hom.: 5106

Bravo AF: 0.325

Asia WGS AF: 0.413 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.76
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs4354072; hg19: chr5-36367860;