rs9530579

chr13-76651467-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648060.1(ENSG00000285572):n.395+77878T>C 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 0.223 in 152,192 control chromosomes in the GnomAD database, including 4,901 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 (4901 hom., cov: 32)
• Consequence: ENST00000648060.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.695

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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
	ENST00000648060.1	n.395+77878T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33920 AN: 152074 Hom.: 4900 Cov.: 32

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.223 AC: 33914 AN: 152192 Hom.: 4901 Cov.: 32 AF XY: 0.222 AC XY: 16555 AN XY: 74406

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.240

Alfa AF: 0.287 Hom.: 3404

Bravo AF: 0.215

Asia WGS AF: 0.131 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	7.2
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9530579; hg19: chr13-77225602;