rs676318

Variant names:

• chr11-68449952-T-C
• rs676318

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.162 AC: 6745 AN: 41542

American (AMR) AF: 0.0744 AC: 1138 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0937 AC: 325 AN: 3470

East Asian (EAS) AF: 0.0114 AC: 59 AN: 5180

South Asian (SAS) AF: 0.0354 AC: 171 AN: 4828

European-Finnish (FIN) AF: 0.0239 AC: 254 AN: 10614

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0730 AC: 4964 AN: 68028

Other (OTH) AF: 0.0890 AC: 188 AN: 2112

Alfa AF: 0.0785 Hom.: 959

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
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs676318; hg19: chr11-68217420;