6-3878280-G-A

Variant names:

• chr6-3878280-G-A
• rs4621668
• ENST00000648025.2:n.245+1129G>A

Variant summary

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

The ENST00000648025.2(ENSG00000233068):​n.245+1129G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,066 control chromosomes in the GnomAD database, including 9,218 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 0.34 (9218 hom., cov: 31)
• Consequence: ENSG00000233068 ENST00000648025.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 2 publications found

Genes affected

ENSG00000233068 (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 (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648025.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000233068	ENST00000648025.2		n.245+1129G>A		intron	N/A
	ENSG00000233068	ENST00000780356.1		n.205+1129G>A		intron	N/A
	ENSG00000233068	ENST00000780357.1		n.119-14782G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51035 AN: 151948 Hom.: 9222 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.336 AC: 51061 AN: 152066 Hom.: 9218 Cov.: 31 AF XY: 0.337 AC XY: 25068 AN XY: 74322

African (AFR) AF: 0.326 AC: 13507 AN: 41474

American (AMR) AF: 0.462 AC: 7063 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3472

East Asian (EAS) AF: 0.598 AC: 3084 AN: 5158

South Asian (SAS) AF: 0.410 AC: 1975 AN: 4820

European-Finnish (FIN) AF: 0.207 AC: 2189 AN: 10582

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20743 AN: 67962

Other (OTH) AF: 0.370 AC: 782 AN: 2112

Alfa AF: 0.309 Hom.: 929

Bravo AF: 0.356

Asia WGS AF: 0.484 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		-0.043

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4621668; hg19: chr6-3878514;