7-46849893-T-C

Position:

• chr7-46849893-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 0.312 in 152,090 control chromosomes in the GnomAD database, including 7,566 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 0.31 (7566 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46849893T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47514 AN: 151972 Hom.: 7570 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.312 AC: 47515 AN: 152090 Hom.: 7566 Cov.: 32 AF XY: 0.313 AC XY: 23236 AN XY: 74352

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.312

Alfa AF: 0.325 Hom.: 4148

Bravo AF: 0.316

Asia WGS AF: 0.398 AC: 1376 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4236383; hg19: chr7-46889491;