7-46871342-T-G

Position:

• chr7-46871342-T-G

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 0.385 in 152,034 control chromosomes in the GnomAD database, including 11,357 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 0.39 (11357 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.46871342T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58489 AN: 151916 Hom.: 11349 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.385 AC: 58539 AN: 152034 Hom.: 11357 Cov.: 32 AF XY: 0.384 AC XY: 28572 AN XY: 74340

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.385

Alfa AF: 0.285 Hom.: 966

Bravo AF: 0.383

Asia WGS AF: 0.328 AC: 1146 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.42
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4637723; hg19: chr7-46910940;