6-21263024-C-T

Variant names:

• chr6-21263024-C-T
• rs4712595
• ENST00000669568.2:n.296+7813G>A

Variant summary

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

The ENST00000669568.2(ENSG00000287404):​n.296+7813G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,024 control chromosomes in the GnomAD database, including 20,305 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 0.49 (20305 hom., cov: 32)
• Consequence: ENSG00000287404 ENST00000669568.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.59 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+7813G>A		intron	N/A
	ENSG00000287404	ENST00000724722.1		n.279+7813G>A		intron	N/A
	ENSG00000287404	ENST00000724723.1		n.123+7813G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75087 AN: 151904 Hom.: 20303 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.494 AC: 75116 AN: 152024 Hom.: 20305 Cov.: 32 AF XY: 0.495 AC XY: 36759 AN XY: 74312

African (AFR) AF: 0.285 AC: 11816 AN: 41452

American (AMR) AF: 0.515 AC: 7869 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1878 AN: 3464

East Asian (EAS) AF: 0.340 AC: 1752 AN: 5160

South Asian (SAS) AF: 0.441 AC: 2122 AN: 4808

European-Finnish (FIN) AF: 0.696 AC: 7337 AN: 10546

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40438 AN: 68004

Other (OTH) AF: 0.495 AC: 1044 AN: 2110

Alfa AF: 0.541 Hom.: 2849

Bravo AF: 0.478

Asia WGS AF: 0.366 AC: 1273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.59
PhyloP100		-1.4

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: rs4712595;

hg19: chr6-21263255;