rs1946518

chr11-112164735-T-G

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 0.594 in 151,882 control chromosomes in the GnomAD database, including 26,910 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 0.59 (26910 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.935

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 = 0.665 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: 0.594 AC: 90083 AN: 151764 Hom.: 26872 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.594 AC: 90174 AN: 151882 Hom.: 26910 Cov.: 31 AF XY: 0.591 AC XY: 43839 AN XY: 74216

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.583

Alfa AF: 0.591 Hom.: 33978

Bravo AF: 0.593

Asia WGS AF: 0.608 AC: 2112 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.5
Dann	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1946518; hg19: chr11-112035458;