7-57316046-A-T

Position:

• chr7-57316046-A-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 0.834 in 152,114 control chromosomes in the GnomAD database, including 53,316 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 0.83 (53316 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57316046A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126682 AN: 151996 Hom.: 53256 Cov.: 32

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.834 AC: 126803 AN: 152114 Hom.: 53316 Cov.: 32 AF XY: 0.837 AC XY: 62213 AN XY: 74370

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.674

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.781

Alfa AF: 0.751 Hom.: 2257

Bravo AF: 0.839

Asia WGS AF: 0.848 AC: 2950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7808342; hg19: chr7-57383753;