rs11043827

Variant names:

• chr12-18065173-A-T
• rs11043827

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 0.255 in 152,004 control chromosomes in the GnomAD database, including 5,552 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 0.26 (5552 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 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: 0.255 AC: 38780 AN: 151886 Hom.: 5553 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.255 AC: 38782 AN: 152004 Hom.: 5552 Cov.: 32 AF XY: 0.253 AC XY: 18823 AN XY: 74298

African (AFR) AF: 0.145 AC: 6003 AN: 41466

American (AMR) AF: 0.376 AC: 5748 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3472

East Asian (EAS) AF: 0.104 AC: 537 AN: 5160

South Asian (SAS) AF: 0.152 AC: 732 AN: 4816

European-Finnish (FIN) AF: 0.225 AC: 2379 AN: 10568

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21011 AN: 67928

Other (OTH) AF: 0.277 AC: 585 AN: 2112

Alfa AF: 0.279 Hom.: 760

Bravo AF: 0.261

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.0
DANN	Benign	0.65
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs11043827; hg19: chr12-18218107;