rs11104632

Variant names:

• chr12-87829908-G-A
• rs11104632

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 0.157 in 151,428 control chromosomes in the GnomAD database, including 2,470 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 0.16 (2470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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: 0.158 AC: 23855 AN: 151312 Hom.: 2470 Cov.: 31

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0409

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.157 AC: 23848 AN: 151428 Hom.: 2470 Cov.: 31 AF XY: 0.152 AC XY: 11234 AN XY: 73968

African (AFR) AF: 0.0428 AC: 1773 AN: 41406

American (AMR) AF: 0.194 AC: 2949 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3462

East Asian (EAS) AF: 0.0410 AC: 210 AN: 5126

South Asian (SAS) AF: 0.0641 AC: 308 AN: 4808

European-Finnish (FIN) AF: 0.169 AC: 1780 AN: 10540

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15597 AN: 67624

Other (OTH) AF: 0.185 AC: 388 AN: 2096

Alfa AF: 0.181 Hom.: 491

Bravo AF: 0.155

Asia WGS AF: 0.0490 AC: 170 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.4
DANN	Benign	0.46
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11104632; hg19: chr12-88223685;