rs9568856

Positions:

• chr13-53490846-G-A
• chr13-53490846-G-C
• chr13-53490846-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000657016.1(ENSG00000287722):​n.629+186724G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 151,818 control chromosomes in the GnomAD database, including 4,421 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 0.22 (4421 hom., cov: 32)
• Consequence: ENST00000657016.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657016.1	n.629+186724G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33009 AN: 151698 Hom.: 4409 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.218 AC: 33066 AN: 151818 Hom.: 4421 Cov.: 32 AF XY: 0.220 AC XY: 16321 AN XY: 74246

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.192

Alfa AF: 0.142 Hom.: 3399

Bravo AF: 0.240

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	14
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9568856; hg19: chr13-54064981;