5-150294411-G-A

Position:

• chr5-150294411-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 0.74 in 152,002 control chromosomes in the GnomAD database, including 43,611 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 0.74 (43611 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430

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 (NFE) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112407 AN: 151884 Hom.: 43616 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.740 AC: 112436 AN: 152002 Hom.: 43611 Cov.: 31 AF XY: 0.738 AC XY: 54830 AN XY: 74270

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.873

Gnomad4 OTH AF: 0.751

Alfa AF: 0.805 Hom.: 8298

Bravo AF: 0.716

Asia WGS AF: 0.735 AC: 2555 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	3.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4958849; hg19: chr5-149673974;