rs11178918

Variant names:

• chr12-71731505-A-G
• rs11178918

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 0.134 in 152,126 control chromosomes in the GnomAD database, including 1,734 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 0.13 (1734 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.365 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: 0.134 AC: 20427 AN: 152006 Hom.: 1734 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.0976

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.134 AC: 20429 AN: 152126 Hom.: 1734 Cov.: 32 AF XY: 0.141 AC XY: 10456 AN XY: 74352

African (AFR) AF: 0.143 AC: 5920 AN: 41520

American (AMR) AF: 0.181 AC: 2762 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0976 AC: 338 AN: 3464

East Asian (EAS) AF: 0.379 AC: 1955 AN: 5152

South Asian (SAS) AF: 0.179 AC: 863 AN: 4818

European-Finnish (FIN) AF: 0.173 AC: 1835 AN: 10578

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.0931 AC: 6329 AN: 67992

Other (OTH) AF: 0.131 AC: 277 AN: 2110

Alfa AF: 0.111 Hom.: 4805

Bravo AF: 0.138

Asia WGS AF: 0.212 AC: 738 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	1.3
DANN	Benign	0.20
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs11178918; hg19: chr12-72125285;