rs1560547

Variant names:

• chr4-186850554-A-G
• rs1560547
• ENST00000839407.1:n.395+9565A>G

Variant summary

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

The ENST00000839407.1(ENSG00000250971):​n.395+9565A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,120 control chromosomes in the GnomAD database, including 58,191 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 0.87 (58191 hom., cov: 31)
• Consequence: ENSG00000250971 ENST00000839407.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 3 publications found

Genes affected

ENSG00000250971 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723906	XR_002959826.2	n.328+9565A>G		intron_variant	Intron 1 of 3
LOC102723906	XR_007058501.1	n.328+9565A>G		intron_variant	Intron 1 of 2
LOC102723906	XR_007058502.1	n.328+9565A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250971	ENST00000839407.1	n.395+9565A>G		intron_variant	Intron 1 of 6
ENSG00000250971	ENST00000839408.1	n.185+9565A>G		intron_variant	Intron 1 of 4
ENSG00000250971	ENST00000839411.1	n.340-2445A>G		intron_variant	Intron 1 of 1
ENSG00000309247	ENST00000839801.1	n.322-4825T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.874 AC: 132779 AN: 152002 Hom.: 58139 Cov.: 31

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.874 AC: 132889 AN: 152120 Hom.: 58191 Cov.: 31 AF XY: 0.876 AC XY: 65119 AN XY: 74368

African (AFR) AF: 0.809 AC: 33543 AN: 41478

American (AMR) AF: 0.871 AC: 13306 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3188 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5141 AN: 5152

South Asian (SAS) AF: 0.901 AC: 4347 AN: 4822

European-Finnish (FIN) AF: 0.910 AC: 9629 AN: 10580

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60769 AN: 68016

Other (OTH) AF: 0.884 AC: 1867 AN: 2112

Alfa AF: 0.884 Hom.: 49873

Bravo AF: 0.866

Asia WGS AF: 0.945 AC: 3286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.78
DANN	Benign	0.46
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1560547; hg19: chr4-187771708;