chr7-24308272-G-T

Position:

• chr7-24308272-G-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 0.223 in 148,774 control chromosomes in the GnomAD database, including 3,848 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 0.22 (3848 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24308272G>T		intergenic_region
LOC107986777	XR_001745121.2	n.209+11085C>A		intron_variant
LOC107986777	XR_001745122.2	n.81-111243C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33131 AN: 148656 Hom.: 3846 Cov.: 28

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.223 AC: 33153 AN: 148774 Hom.: 3848 Cov.: 28 AF XY: 0.223 AC XY: 16102 AN XY: 72318

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.250

Alfa AF: 0.241 Hom.: 7894

Bravo AF: 0.212

Asia WGS AF: 0.302 AC: 1050 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.92
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16089; hg19: chr7-24347891;