rs12118986

Variant names:

• chr1-61638142-C-A
• rs12118986
• ENST00000823956.1:n.50+5602G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-61638142-C-A
• chr1-61638142-C-G

Variant summary

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

The ENST00000823956.1(ENSG00000287224):​n.50+5602G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0399 in 152,198 control chromosomes in the GnomAD database, including 196 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 0.040 (196 hom., cov: 32)
• Consequence: ENSG00000287224 ENST00000823956.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 1 publications found

Genes affected

ENSG00000287224 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823956.1. 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
	ENSG00000287224	ENST00000823956.1		n.50+5602G>T		intron	N/A
	ENSG00000287224	ENST00000823957.1		n.89+3714G>T		intron	N/A
	ENSG00000287224	ENST00000823958.1		n.62+3714G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0399 AC: 6073 AN: 152080 Hom.: 196 Cov.: 32

Gnomad AFR AF: 0.00961

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0300

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0399 AC: 6075 AN: 152198 Hom.: 196 Cov.: 32 AF XY: 0.0407 AC XY: 3026 AN XY: 74390

African (AFR) AF: 0.00959 AC: 398 AN: 41516

American (AMR) AF: 0.0300 AC: 458 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0188 AC: 91 AN: 4830

European-Finnish (FIN) AF: 0.0851 AC: 901 AN: 10582

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0599 AC: 4076 AN: 68010

Other (OTH) AF: 0.0312 AC: 66 AN: 2114

Alfa AF: 0.0512 Hom.: 154

Bravo AF: 0.0329

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.4
DANN	Benign	0.48
PhyloP100		0.50

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: rs12118986;

hg19: chr1-62103814;