ENST00000755446.1:n.327-878G>A

Variant names:

• chr6-31381102-G-A
• rs2844538
• ENST00000755446.1:n.327-878G>A

Variant summary

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

The ENST00000755446.1(ENSG00000298426):​n.327-878G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,718 control chromosomes in the GnomAD database, including 28,500 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 0.61 (28500 hom., cov: 31)
• Consequence: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 4 publications found

Genes affected

ENSG00000298426 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755446.1. 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
	ENSG00000298426	ENST00000755446.1		n.327-878G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91840 AN: 151610 Hom.: 28472 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.606 AC: 91910 AN: 151718 Hom.: 28500 Cov.: 31 AF XY: 0.608 AC XY: 45055 AN XY: 74154

African (AFR) AF: 0.486 AC: 20078 AN: 41340

American (AMR) AF: 0.639 AC: 9749 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2534 AN: 3470

East Asian (EAS) AF: 0.544 AC: 2816 AN: 5174

South Asian (SAS) AF: 0.654 AC: 3152 AN: 4820

European-Finnish (FIN) AF: 0.700 AC: 7277 AN: 10396

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.649 AC: 44061 AN: 67936

Other (OTH) AF: 0.590 AC: 1247 AN: 2112

Alfa AF: 0.593 Hom.: 13125

Bravo AF: 0.591

Asia WGS AF: 0.605 AC: 2106 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2844538; hg19: chr6-31348879;