chr5-18676174-T-C

Variant names:

• chr5-18676174-T-C
• rs6894312
• ENST00000761647.1:n.53-1303A>G

Variant summary

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

The ENST00000761647.1(ENSG00000299222):​n.53-1303A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 151,882 control chromosomes in the GnomAD database, including 56,761 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 0.86 (56761 hom., cov: 31)
• Consequence: ENSG00000299222 ENST00000761647.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 1 publications found

Genes affected

ENSG00000299222 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761647.1. 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
	ENSG00000299222	ENST00000761647.1		n.53-1303A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130696 AN: 151764 Hom.: 56694 Cov.: 31

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.861 AC: 130823 AN: 151882 Hom.: 56761 Cov.: 31 AF XY: 0.861 AC XY: 63908 AN XY: 74216

African (AFR) AF: 0.959 AC: 39783 AN: 41498

American (AMR) AF: 0.861 AC: 13140 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2739 AN: 3466

East Asian (EAS) AF: 0.916 AC: 4721 AN: 5156

South Asian (SAS) AF: 0.858 AC: 4123 AN: 4808

European-Finnish (FIN) AF: 0.819 AC: 8619 AN: 10526

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55035 AN: 67852

Other (OTH) AF: 0.861 AC: 1816 AN: 2108

Alfa AF: 0.833 Hom.: 4675

Bravo AF: 0.867

Asia WGS AF: 0.903 AC: 3130 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.62
PhyloP100		-0.65

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: rs6894312;

hg19: chr5-18676283;