chr6-24721439-A-T

Position:

• chr6-24721439-A-T

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 0.178 in 152,214 control chromosomes in the GnomAD database, including 2,578 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 0.18 (2578 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24721439A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27134 AN: 152096 Hom.: 2576 Cov.: 33

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.178 AC: 27158 AN: 152214 Hom.: 2578 Cov.: 33 AF XY: 0.178 AC XY: 13242 AN XY: 74416

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.0119

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.173

Alfa AF: 0.126 Hom.: 220

Bravo AF: 0.171

Asia WGS AF: 0.0620 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.2
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923187; hg19: chr6-24721667;