rs11713590

Variant names:

• chr3-5689455-G-A
• rs11713590
• ENST00000425894.2:n.183-6923G>A

Variant summary

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

The ENST00000425894.2(ENSG00000229642):​n.183-6923G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,052 control chromosomes in the GnomAD database, including 31,869 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 0.64 (31869 hom., cov: 32)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 1 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376939	XR_940571.3	n.204+1274G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229642	ENST00000425894.2	n.183-6923G>A		intron_variant	Intron 1 of 8	3
ENSG00000229642	ENST00000779001.1	n.104-6923G>A		intron_variant	Intron 1 of 7
ENSG00000229642	ENST00000779002.1	n.124-6923G>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96521 AN: 151936 Hom.: 31807 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.636 AC: 96651 AN: 152052 Hom.: 31869 Cov.: 32 AF XY: 0.639 AC XY: 47473 AN XY: 74330

African (AFR) AF: 0.805 AC: 33417 AN: 41512

American (AMR) AF: 0.615 AC: 9389 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1708 AN: 3472

East Asian (EAS) AF: 0.896 AC: 4633 AN: 5170

South Asian (SAS) AF: 0.637 AC: 3070 AN: 4818

European-Finnish (FIN) AF: 0.579 AC: 6108 AN: 10554

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.536 AC: 36422 AN: 67940

Other (OTH) AF: 0.598 AC: 1263 AN: 2112

Alfa AF: 0.568 Hom.: 97031

Bravo AF: 0.648

Asia WGS AF: 0.756 AC: 2625 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.29
DANN	Benign	0.58
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11713590; hg19: chr3-5731142;