ENST00000656085.1:n.42+22389G>A

Variant names:

• chr6-159640197-C-T
• rs7754295
• ENST00000656085.1:n.42+22389G>A

Variant summary

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

The ENST00000656085.1(ENSG00000286533):​n.42+22389G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0895 in 152,082 control chromosomes in the GnomAD database, including 821 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 0.089 (821 hom., cov: 32)
• Consequence: ENSG00000286533 ENST00000656085.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.548
• Publications: 8 publications found

Genes affected

ENSG00000286533 (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 (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656085.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286533	ENST00000656085.1		n.42+22389G>A		intron	N/A
	ENSG00000286533	ENST00000794978.1		n.185+22286G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0894 AC: 13587 AN: 151964 Hom.: 818 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.0895 AC: 13610 AN: 152082 Hom.: 821 Cov.: 32 AF XY: 0.0890 AC XY: 6618 AN XY: 74360

African (AFR) AF: 0.169 AC: 7003 AN: 41454

American (AMR) AF: 0.0618 AC: 944 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0450 AC: 156 AN: 3470

East Asian (EAS) AF: 0.102 AC: 526 AN: 5168

South Asian (SAS) AF: 0.0859 AC: 413 AN: 4806

European-Finnish (FIN) AF: 0.0438 AC: 464 AN: 10586

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0562 AC: 3821 AN: 68006

Other (OTH) AF: 0.0805 AC: 170 AN: 2112

Alfa AF: 0.0678 Hom.: 1922

Bravo AF: 0.0935

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.73
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs7754295; hg19: chr6-160061229;