rs715412

Variant names:

• chr11-118813901-G-A
• rs715412

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 0.17 in 152,196 control chromosomes in the GnomAD database, including 2,431 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 0.17 (2431 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 17 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 (SAS) allele frequency at 95% confidence interval = 0.221 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: 0.170 AC: 25808 AN: 152078 Hom.: 2428 Cov.: 32

Gnomad AFR AF: 0.0805

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.170 AC: 25812 AN: 152196 Hom.: 2431 Cov.: 32 AF XY: 0.171 AC XY: 12740 AN XY: 74396

African (AFR) AF: 0.0804 AC: 3338 AN: 41542

American (AMR) AF: 0.172 AC: 2622 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3468

East Asian (EAS) AF: 0.140 AC: 724 AN: 5182

South Asian (SAS) AF: 0.232 AC: 1119 AN: 4824

European-Finnish (FIN) AF: 0.224 AC: 2371 AN: 10590

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14393 AN: 67998

Other (OTH) AF: 0.162 AC: 342 AN: 2114

Alfa AF: 0.203 Hom.: 1780

Bravo AF: 0.158

Asia WGS AF: 0.174 AC: 603 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	0.45
DANN	Benign	0.36
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs715412; hg19: chr11-118684610;