rs1946519

chr11-112164784-A-C

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 152,002 control chromosomes in the GnomAD database, including 26,943 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 (26943 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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: 90160 AN: 151884 Hom.: 26905 Cov.: 32

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.536

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: 90251 AN: 152002 Hom.: 26943 Cov.: 32 AF XY: 0.591 AC XY: 43880 AN XY: 74274

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.595

Gnomad4 OTH AF: 0.583

Alfa AF: 0.591 Hom.: 16353

Bravo AF: 0.593

Asia WGS AF: 0.609 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.7
Dann	Benign	0.70

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: rs1946519; hg19: chr11-112035507;