rs4304924

Variant names:

• chr13-78664790-G-A
• rs4304924

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.530

Alfa AF: 0.544 Hom.: 14437

Bravo AF: 0.460

Asia WGS AF: 0.365 AC: 1271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4304924; hg19: chr13-79238925;