6-21258023-T-C

Variant names:

• chr6-21258023-T-C
• rs2876587
• ENST00000669568.2:n.296+12814A>G

Variant summary

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

The ENST00000669568.2(ENSG00000287404):​n.296+12814A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,068 control chromosomes in the GnomAD database, including 50,036 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 0.81 (50036 hom., cov: 31)
• Consequence: ENSG00000287404 ENST00000669568.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 1 publications found

Genes affected

ENSG00000287404 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669568.2. 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
	ENSG00000287404	ENST00000669568.2		n.296+12814A>G		intron	N/A
	ENSG00000287404	ENST00000724722.1		n.279+12814A>G		intron	N/A
	ENSG00000287404	ENST00000724723.1		n.123+12814A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122530 AN: 151950 Hom.: 49996 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.806 AC: 122627 AN: 152068 Hom.: 50036 Cov.: 31 AF XY: 0.804 AC XY: 59798 AN XY: 74374

African (AFR) AF: 0.683 AC: 28291 AN: 41416

American (AMR) AF: 0.766 AC: 11720 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2795 AN: 3472

East Asian (EAS) AF: 0.760 AC: 3934 AN: 5178

South Asian (SAS) AF: 0.796 AC: 3827 AN: 4808

European-Finnish (FIN) AF: 0.881 AC: 9320 AN: 10584

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.881 AC: 59877 AN: 67996

Other (OTH) AF: 0.823 AC: 1742 AN: 2116

Alfa AF: 0.846 Hom.: 12552

Bravo AF: 0.794

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.78
PhyloP100		-0.021

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: rs2876587;

hg19: chr6-21258254;