rs676318

Variant names:

• chr11-68449952-T-C
• rs676318

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;