rs981579

Variant names:

• chr4-28543605-A-G
• rs981579
• ENST00000509416.1:n.403-34311A>G

Variant summary

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

The ENST00000509416.1(ENSG00000250064):​n.403-34311A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,962 control chromosomes in the GnomAD database, including 5,369 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 0.24 (5369 hom., cov: 32)
• Consequence: ENSG00000250064 ENST00000509416.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 1 publications found

Genes affected

ENSG00000250064 (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 (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509416.1. 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
	LOC105374557	NR_188396.1		n.348-34311A>G		intron	N/A
	LOC105374557	NR_188397.1		n.348-56442A>G		intron	N/A
	LOC105374557	NR_188399.1		n.301-56442A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250064	ENST00000509416.1	TSL:3	n.403-34311A>G		intron	N/A
	ENSG00000250064	ENST00000729962.1		n.219-34311A>G		intron	N/A
	ENSG00000250064	ENST00000729963.1		n.211-8770A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36494 AN: 151844 Hom.: 5360 Cov.: 32

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.240 AC: 36521 AN: 151962 Hom.: 5369 Cov.: 32 AF XY: 0.244 AC XY: 18092 AN XY: 74264

African (AFR) AF: 0.0784 AC: 3253 AN: 41510

American (AMR) AF: 0.358 AC: 5445 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3472

East Asian (EAS) AF: 0.555 AC: 2864 AN: 5158

South Asian (SAS) AF: 0.388 AC: 1872 AN: 4824

European-Finnish (FIN) AF: 0.257 AC: 2714 AN: 10574

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18407 AN: 67892

Other (OTH) AF: 0.264 AC: 558 AN: 2112

Alfa AF: 0.260 Hom.: 1054

Bravo AF: 0.241

Asia WGS AF: 0.470 AC: 1629 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.45
PhyloP100		-0.10

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs981579;

hg19: chr4-28545227;