rs12807809

Variant names:

• chr11-124736389-T-C
• rs12807809
• ENST00000844206.1:n.180-3523T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000844206.1(ENSG00000309835):​n.180-3523T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,126 control chromosomes in the GnomAD database, including 3,172 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 0.20 (3172 hom., cov: 32)
• Consequence: ENSG00000309835 ENST00000844206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 96 publications found

Genes affected

ENSG00000309835 (HGNC:):

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 = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844206.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309835	ENST00000844206.1		n.180-3523T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30021 AN: 152008 Hom.: 3158 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.198 AC: 30085 AN: 152126 Hom.: 3172 Cov.: 32 AF XY: 0.196 AC XY: 14550 AN XY: 74372

African (AFR) AF: 0.263 AC: 10895 AN: 41468

American (AMR) AF: 0.169 AC: 2577 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1489 AN: 5174

South Asian (SAS) AF: 0.0976 AC: 471 AN: 4828

European-Finnish (FIN) AF: 0.170 AC: 1801 AN: 10596

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11667 AN: 67996

Other (OTH) AF: 0.199 AC: 419 AN: 2108

Alfa AF: 0.178 Hom.: 11317

Bravo AF: 0.201

Asia WGS AF: 0.244 AC: 851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.62
PhyloP100		-0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12807809;

hg19: chr11-124606285;