7-24282719-T-C

Position:

• chr7-24282719-T-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 0.429 in 151,920 control chromosomes in the GnomAD database, including 14,916 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 0.43 (14916 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24282719T>C		intergenic_region
LOC107986777	XR_001745121.2	n.209+36638A>G		intron_variant
LOC107986777	XR_001745122.2	n.81-85690A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65108 AN: 151800 Hom.: 14884 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.429 AC: 65199 AN: 151920 Hom.: 14916 Cov.: 32 AF XY: 0.438 AC XY: 32500 AN XY: 74278

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.424

Alfa AF: 0.405 Hom.: 2326

Bravo AF: 0.439

Asia WGS AF: 0.673 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.039
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16148; hg19: chr7-24322338;