rs4773068

chr13-109636620-G-Achr13-109636620-G-T

Variant summary

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

The ENST00000650264.1(ENSG00000285534):n.759-65462C>T 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 0.0843 in 152,112 control chromosomes in the GnomAD database, including 801 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 0.084 (801 hom., cov: 33)
• Consequence: ENST00000650264.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 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
	ENST00000650264.1	n.759-65462C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0843 AC: 12806 AN: 151994 Hom.: 795 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0591

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0391

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.0843 AC: 12830 AN: 152112 Hom.: 801 Cov.: 33 AF XY: 0.0876 AC XY: 6509 AN XY: 74340

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0591

Gnomad4 NFE AF: 0.0391

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.0478 Hom.: 79

Bravo AF: 0.0917

Asia WGS AF: 0.234 AC: 812 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.71
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4773068; hg19: chr13-110288967;