chr3-117224163-T-C

Position:

• chr3-117224163-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 0.428 in 152,084 control chromosomes in the GnomAD database, including 14,763 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 (14763 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117224163T>C		intergenic_region
LOC124909415	XR_007096015.1	n.29329+24853A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65075 AN: 151966 Hom.: 14736 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.428 AC: 65147 AN: 152084 Hom.: 14763 Cov.: 32 AF XY: 0.428 AC XY: 31793 AN XY: 74362

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.450

Alfa AF: 0.369 Hom.: 21539

Bravo AF: 0.449

Asia WGS AF: 0.552 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1462845; hg19: chr3-116943010;