5-90036907-C-T

Variant names:

• chr5-90036907-C-T
• rs157568

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 0.331 in 152,036 control chromosomes in the GnomAD database, including 12,251 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 0.33 (12251 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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: 0.331 AC: 50238 AN: 151916 Hom.: 12206 Cov.: 33

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.331 AC: 50329 AN: 152036 Hom.: 12251 Cov.: 33 AF XY: 0.330 AC XY: 24539 AN XY: 74344

African (AFR) AF: 0.690 AC: 28612 AN: 41452

American (AMR) AF: 0.264 AC: 4028 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3472

East Asian (EAS) AF: 0.105 AC: 545 AN: 5184

South Asian (SAS) AF: 0.329 AC: 1583 AN: 4818

European-Finnish (FIN) AF: 0.178 AC: 1877 AN: 10570

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.173 AC: 11752 AN: 67954

Other (OTH) AF: 0.297 AC: 627 AN: 2114

Alfa AF: 0.105 Hom.: 159

Bravo AF: 0.349

Asia WGS AF: 0.245 AC: 854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.56
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs157568; hg19: chr5-89332724;