ENST00000549660.1:n.130-1700G>A

Variant names:

• chr12-32991864-G-A
• rs983579
• ENST00000549660.1:n.130-1700G>A

Variant summary

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

The ENST00000549660.1(ENSG00000257435):​n.130-1700G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 152,014 control chromosomes in the GnomAD database, including 366 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 0.056 (366 hom., cov: 32)
• Consequence: ENSG00000257435 ENST00000549660.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.765
• Publications: 1 publications found

Genes affected

ENSG00000257435 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.084 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549660.1. 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
	ENSG00000257435	ENST00000549660.1	TSL:4	n.130-1700G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8553 AN: 151898 Hom.: 366 Cov.: 32

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0491

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0266

Gnomad FIN AF: 0.0534

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0562 AC: 8549 AN: 152014 Hom.: 366 Cov.: 32 AF XY: 0.0552 AC XY: 4100 AN XY: 74274

African (AFR) AF: 0.0140 AC: 579 AN: 41464

American (AMR) AF: 0.0490 AC: 748 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3464

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5172

South Asian (SAS) AF: 0.0264 AC: 127 AN: 4804

European-Finnish (FIN) AF: 0.0534 AC: 564 AN: 10564

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.0858 AC: 5835 AN: 67984

Other (OTH) AF: 0.0629 AC: 132 AN: 2100

Alfa AF: 0.0705 Hom.: 304

Bravo AF: 0.0552

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.61
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs983579; hg19: chr12-33144798;