rs11959615

chr5-148821753-T-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 0.596 in 152,036 control chromosomes in the GnomAD database, including 27,380 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 (27380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 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: 0.596 AC: 90487 AN: 151918 Hom.: 27362 Cov.: 32

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.596 AC: 90551 AN: 152036 Hom.: 27380 Cov.: 32 AF XY: 0.603 AC XY: 44823 AN XY: 74294

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.627

Alfa AF: 0.575 Hom.: 3168

Bravo AF: 0.596

Asia WGS AF: 0.747 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	11
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11959615; hg19: chr5-148201316;