rs4942859

Variant names:

• chr13-49624022-G-A
• rs4942859
• ENST00000821102.1:n.36-3233C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-49624022-G-A
• chr13-49624022-G-T

Variant summary

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

The ENST00000821102.1(ENSG00000306783):​n.36-3233C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 151,982 control chromosomes in the GnomAD database, including 18,834 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 0.48 (18834 hom., cov: 31)
• Consequence: ENSG00000306783 ENST00000821102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.735
• Publications: 15 publications found

Genes affected

ENSG00000306783 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821102.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306783	ENST00000821102.1		n.36-3233C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73412 AN: 151862 Hom.: 18817 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.483 AC: 73450 AN: 151982 Hom.: 18834 Cov.: 31 AF XY: 0.472 AC XY: 35083 AN XY: 74256

African (AFR) AF: 0.338 AC: 13999 AN: 41428

American (AMR) AF: 0.524 AC: 8005 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1683 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1414 AN: 5166

South Asian (SAS) AF: 0.329 AC: 1585 AN: 4822

European-Finnish (FIN) AF: 0.442 AC: 4660 AN: 10550

Middle Eastern (MID) AF: 0.517 AC: 151 AN: 292

European-Non Finnish (NFE) AF: 0.596 AC: 40482 AN: 67964

Other (OTH) AF: 0.507 AC: 1070 AN: 2110

Alfa AF: 0.548 Hom.: 73611

Bravo AF: 0.485

Asia WGS AF: 0.308 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	12
DANN	Benign	0.86
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs4942859; hg19: chr13-50198158;