rs568529

Variant names:

• chr11-34820959-C-A
• rs568529
• ENST00000843048.1:n.657-56051C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-34820959-C-A
• chr11-34820959-C-G
• chr11-34820959-C-T

Variant summary

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

The ENST00000843048.1(ENSG00000309692):​n.657-56051C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 151,962 control chromosomes in the GnomAD database, including 35,661 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 0.68 (35661 hom., cov: 31)
• Consequence: ENSG00000309692 ENST00000843048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 6 publications found

Genes affected

ENSG00000309692 (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 = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723568	XR_007062652.1	n.1045-56051C>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309692	ENST00000843048.1	n.657-56051C>A		intron_variant	Intron 2 of 2
ENSG00000309692	ENST00000843049.1	n.849-56051C>A		intron_variant	Intron 3 of 3
ENSG00000309692	ENST00000843050.1	n.441-56051C>A		intron_variant	Intron 3 of 3
ENSG00000309692	ENST00000843051.1	n.299-56051C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103771 AN: 151844 Hom.: 35665 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.709

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.683 AC: 103800 AN: 151962 Hom.: 35661 Cov.: 31 AF XY: 0.681 AC XY: 50572 AN XY: 74244

African (AFR) AF: 0.640 AC: 26484 AN: 41400

American (AMR) AF: 0.644 AC: 9844 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2429 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4289 AN: 5180

South Asian (SAS) AF: 0.608 AC: 2926 AN: 4810

European-Finnish (FIN) AF: 0.704 AC: 7418 AN: 10540

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.709 AC: 48218 AN: 67968

Other (OTH) AF: 0.663 AC: 1397 AN: 2108

Alfa AF: 0.697 Hom.: 18404

Bravo AF: 0.679

Asia WGS AF: 0.683 AC: 2373 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	0.35
DANN	Benign	0.34
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs568529; hg19: chr11-34842506;