chr5-151098757-G-A

Position:

• chr5-151098757-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 0.0722 in 152,206 control chromosomes in the GnomAD database, including 419 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 0.072 (419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 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: 0.0722 AC: 10986 AN: 152088 Hom.: 419 Cov.: 32

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0646

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.0722 AC: 10986 AN: 152206 Hom.: 419 Cov.: 32 AF XY: 0.0736 AC XY: 5476 AN XY: 74402

Gnomad4 AFR AF: 0.0916

Gnomad4 AMR AF: 0.0459

Gnomad4 ASJ AF: 0.0859

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0646

Gnomad4 NFE AF: 0.0591

Gnomad4 OTH AF: 0.0843

Alfa AF: 0.0642 Hom.: 696

Bravo AF: 0.0697

Asia WGS AF: 0.205 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17728338; hg19: chr5-150478318;