chr4-24789058-T-A

Position:

• chr4-24789058-T-A

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 0.264 in 151,914 control chromosomes in the GnomAD database, including 6,063 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 0.26 (6063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40065 AN: 151796 Hom.: 6058 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.264 AC: 40085 AN: 151914 Hom.: 6063 Cov.: 32 AF XY: 0.263 AC XY: 19534 AN XY: 74268

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.287

Alfa AF: 0.144 Hom.: 287

Bravo AF: 0.264

Asia WGS AF: 0.437 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17622933; hg19: chr4-24790680;