11-117878405-C-G

Variant names:

• chr11-117878405-C-G
• rs3809042

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 0.033 in 152,288 control chromosomes in the GnomAD database, including 133 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 0.033 (133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 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: 0.0330 AC: 5025 AN: 152170 Hom.: 134 Cov.: 32

Gnomad AFR AF: 0.00702

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0282

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

GnomAD4 genome AF: 0.0330 AC: 5023 AN: 152288 Hom.: 133 Cov.: 32 AF XY: 0.0343 AC XY: 2552 AN XY: 74458

African (AFR) AF: 0.00700 AC: 291 AN: 41554

American (AMR) AF: 0.0328 AC: 502 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3472

East Asian (EAS) AF: 0.152 AC: 785 AN: 5176

South Asian (SAS) AF: 0.0766 AC: 369 AN: 4818

European-Finnish (FIN) AF: 0.0516 AC: 547 AN: 10606

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2366 AN: 68036

Other (OTH) AF: 0.0288 AC: 61 AN: 2116

Alfa AF: 0.0120 Hom.: 4

Bravo AF: 0.0315

Asia WGS AF: 0.111 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs3809042; hg19: chr11-117749120;