rs676318

Positions:

• chr11-68449952-T-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 0.0917 in 152,272 control chromosomes in the GnomAD database, including 810 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 0.092 (810 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0916 AC: 13931 AN: 152154 Hom.: 804 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.0937

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.0239

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0730

Gnomad OTH AF: 0.0900

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

GnomAD4 genome AF: 0.0917 AC: 13957 AN: 152272 Hom.: 810 Cov.: 31 AF XY: 0.0894 AC XY: 6654 AN XY: 74452

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0744

Gnomad4 ASJ AF: 0.0937

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0354

Gnomad4 FIN AF: 0.0239

Gnomad4 NFE AF: 0.0730

Gnomad4 OTH AF: 0.0890

Alfa AF: 0.0765 Hom.: 643

Bravo AF: 0.100

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.082
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs676318; hg19: chr11-68217420;