rs4942577

Variant names:

• chr13-46823319-C-T
• rs4942577
• ENST00000783844.1:n.96-7977C>T

Variant summary

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

The ENST00000783844.1(ENSG00000302073):​n.96-7977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,134 control chromosomes in the GnomAD database, including 39,979 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 0.72 (39979 hom., cov: 32)
• Consequence: ENSG00000302073 ENST00000783844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 9 publications found

Genes affected

ENSG00000302073 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302073	ENST00000783844.1	n.96-7977C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108840 AN: 152016 Hom.: 39941 Cov.: 32

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.716 AC: 108931 AN: 152134 Hom.: 39979 Cov.: 32 AF XY: 0.707 AC XY: 52607 AN XY: 74378

African (AFR) AF: 0.863 AC: 35837 AN: 41524

American (AMR) AF: 0.700 AC: 10698 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2680 AN: 3470

East Asian (EAS) AF: 0.645 AC: 3332 AN: 5164

South Asian (SAS) AF: 0.608 AC: 2932 AN: 4824

European-Finnish (FIN) AF: 0.518 AC: 5484 AN: 10580

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45603 AN: 67970

Other (OTH) AF: 0.736 AC: 1554 AN: 2110

Alfa AF: 0.693 Hom.: 69989

Bravo AF: 0.740

Asia WGS AF: 0.635 AC: 2209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.86
DANN	Benign	0.31
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs4942577; hg19: chr13-47397454;