rs1319730

Variant names:

• chr11-114027945-A-C
• rs1319730

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;