rs12800641

Variant names:

• chr11-74442195-G-A
• rs12800641
• ENST00000533008.1:n.155-41982G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-74442195-G-A
• chr11-74442195-G-C
• chr11-74442195-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000533008.1(ENSG00000254631):​n.155-41982G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 148,886 control chromosomes in the GnomAD database, including 2,822 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 (2822 hom., cov: 28)
• Consequence: ENSG00000254631 ENST00000533008.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

ENSG00000254631 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 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
ENSG00000254631	ENST00000533008.1	n.155-41982G>A		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.167 AC: 24880 AN: 148768 Hom.: 2812 Cov.: 28

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.0502

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.260

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.167 AC: 24920 AN: 148886 Hom.: 2822 Cov.: 28 AF XY: 0.163 AC XY: 11843 AN XY: 72630

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.0499

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.0523

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.175

Alfa AF: 0.136 Hom.: 1803

Bravo AF: 0.185

Asia WGS AF: 0.132 AC: 457 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12800641; hg19: chr11-74153240;