rs4304924

Variant names:

• chr13-78664790-G-A
• rs4304924
• ENST00000740072.1:n.147-2606G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-78664790-G-A
• chr13-78664790-G-C

Variant summary

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

The ENST00000740072.1(ENSG00000296519):​n.147-2606G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 151,446 control chromosomes in the GnomAD database, including 17,877 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 0.47 (17877 hom., cov: 31)
• Consequence: ENSG00000296519 ENST00000740072.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 17 publications found

Genes affected

ENSG00000296519 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740072.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296519	ENST00000740072.1		n.147-2606G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70723 AN: 151328 Hom.: 17882 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.467 AC: 70723 AN: 151446 Hom.: 17877 Cov.: 31 AF XY: 0.461 AC XY: 34079 AN XY: 73996

African (AFR) AF: 0.299 AC: 12240 AN: 40938

American (AMR) AF: 0.461 AC: 7036 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2201 AN: 3472

East Asian (EAS) AF: 0.249 AC: 1283 AN: 5144

South Asian (SAS) AF: 0.515 AC: 2480 AN: 4814

European-Finnish (FIN) AF: 0.413 AC: 4355 AN: 10548

Middle Eastern (MID) AF: 0.692 AC: 202 AN: 292

European-Non Finnish (NFE) AF: 0.576 AC: 39144 AN: 67966

Other (OTH) AF: 0.530 AC: 1115 AN: 2104

Alfa AF: 0.534 Hom.: 26335

Bravo AF: 0.460

Asia WGS AF: 0.365 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.8
DANN	Benign	0.76
PhyloP100		0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4304924;

hg19: chr13-79238925;