ENST00000755446.1:n.327-609G>A

Variant names:

• chr6-31381371-G-A
• rs76546355
• ENST00000755446.1:n.327-609G>A

Variant summary

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

The ENST00000755446.1(ENSG00000298426):​n.327-609G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0504 in 152,194 control chromosomes in the GnomAD database, including 288 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 0.050 (288 hom., cov: 33)
• Consequence: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 20 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298426	ENST00000755446.1		n.327-609G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0504 AC: 7668 AN: 152076 Hom.: 287 Cov.: 33

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0682

Gnomad ASJ AF: 0.0472

Gnomad EAS AF: 0.0594

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0504 AC: 7669 AN: 152194 Hom.: 288 Cov.: 33 AF XY: 0.0522 AC XY: 3881 AN XY: 74414

African (AFR) AF: 0.0111 AC: 459 AN: 41506

American (AMR) AF: 0.0680 AC: 1040 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0472 AC: 164 AN: 3472

East Asian (EAS) AF: 0.0598 AC: 310 AN: 5186

South Asian (SAS) AF: 0.125 AC: 600 AN: 4818

European-Finnish (FIN) AF: 0.0649 AC: 686 AN: 10570

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0618 AC: 4201 AN: 68028

Other (OTH) AF: 0.0696 AC: 147 AN: 2112

Alfa AF: 0.0503 Hom.: 38

Bravo AF: 0.0491

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs76546355; hg19: chr6-31349148;