rs1319730

chr11-114027945-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.947 in 152,290 control chromosomes in the GnomAD database, including 68,542 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 0.95 (68542 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.978 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: 0.947 AC: 144168 AN: 152172 Hom.: 68506 Cov.: 33

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.996

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.993

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.947 AC: 144260 AN: 152290 Hom.: 68542 Cov.: 33 AF XY: 0.946 AC XY: 70462 AN XY: 74454

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.996

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 0.993

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.951

Alfa AF: 0.970 Hom.: 40548

Bravo AF: 0.931

Asia WGS AF: 0.915 AC: 3185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
Cadd	Benign	18
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1319730; hg19: chr11-113898667;