rs12327091

Variant names:

• chr18-43842486-C-A
• rs12327091
• ENST00000750850.1:n.152-31709G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-43842486-C-A
• chr18-43842486-C-G
• chr18-43842486-C-T

Variant summary

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

The ENST00000750850.1(ENSG00000297765):​n.152-31709G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0822 in 151,482 control chromosomes in the GnomAD database, including 639 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 0.082 (639 hom., cov: 32)
• Consequence: ENSG00000297765 ENST00000750850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 0 publications found

Genes affected

ENSG00000297765 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750850.1. 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
	ENSG00000297765	ENST00000750850.1		n.152-31709G>T		intron	N/A
	ENSG00000297765	ENST00000750851.1		n.255-31709G>T		intron	N/A
	ENSG00000297765	ENST00000750852.1		n.237+4835G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12463 AN: 151358 Hom.: 641 Cov.: 32

Gnomad AFR AF: 0.0286

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0987

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0454

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0983

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0955

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

GnomAD4 genome AF: 0.0822 AC: 12458 AN: 151482 Hom.: 639 Cov.: 32 AF XY: 0.0804 AC XY: 5952 AN XY: 74016

African (AFR) AF: 0.0286 AC: 1185 AN: 41456

American (AMR) AF: 0.116 AC: 1765 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0987 AC: 342 AN: 3464

East Asian (EAS) AF: 0.112 AC: 579 AN: 5148

South Asian (SAS) AF: 0.0458 AC: 219 AN: 4780

European-Finnish (FIN) AF: 0.0925 AC: 966 AN: 10442

Middle Eastern (MID) AF: 0.0935 AC: 20 AN: 214

European-Non Finnish (NFE) AF: 0.103 AC: 7010 AN: 67754

Other (OTH) AF: 0.0944 AC: 197 AN: 2086

Alfa AF: 0.0739 Hom.: 341

Bravo AF: 0.0842

Asia WGS AF: 0.0680 AC: 232 AN: 3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.14
PhyloP100		-0.77

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: rs12327091;

hg19: chr18-41422451;