5-31089242-G-A

Position:

• chr5-31089242-G-A

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 0.124 in 152,168 control chromosomes in the GnomAD database, including 1,332 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 0.12 (1332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

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: 0.124 AC: 18903 AN: 152050 Hom.: 1333 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.0709

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.124 AC: 18914 AN: 152168 Hom.: 1332 Cov.: 32 AF XY: 0.126 AC XY: 9403 AN XY: 74382

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0707

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.0852

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.111

Alfa AF: 0.117 Hom.: 429

Bravo AF: 0.115

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.2
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13355548; hg19: chr5-31089349;