rs31428

chr5-132090586-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0267 in 152,306 control chromosomes in the GnomAD database, including 88 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 0.027 (88 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0267 (4064/152306) while in subpopulation NFE AF= 0.0398 (2706/68026). AF 95% confidence interval is 0.0385. There are 88 homozygotes in gnomad4. There are 1991 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 88 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0267 AC: 4065 AN: 152188 Hom.: 88 Cov.: 32

Gnomad AFR AF: 0.00533

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0168

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.000576

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0267 AC: 4064 AN: 152306 Hom.: 88 Cov.: 32 AF XY: 0.0267 AC XY: 1991 AN XY: 74476

Gnomad4 AFR AF: 0.00532

Gnomad4 AMR AF: 0.0168

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.0586

Gnomad4 NFE AF: 0.0398

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0408 Hom.: 25

Bravo AF: 0.0222

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	7.7
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31428; hg19: chr5-131426279;