rs1150461

chr5-5911268-A-Gchr5-5911268-A-T

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 0.602 in 151,974 control chromosomes in the GnomAD database, including 27,863 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 0.60 (27863 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.699 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: 0.602 AC: 91379 AN: 151858 Hom.: 27834 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.602 AC: 91448 AN: 151974 Hom.: 27863 Cov.: 32 AF XY: 0.609 AC XY: 45198 AN XY: 74270

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.676

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.666

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.642

Alfa AF: 0.602 Hom.: 12478

Bravo AF: 0.597

Asia WGS AF: 0.652 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.3
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1150461; hg19: chr5-5911381;