7-57316046-A-T

Variant names:

• chr7-57316046-A-T
• rs7808342

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;