rs1583830

chr7-155044300-G-Achr7-155044300-G-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 0.51 in 151,868 control chromosomes in the GnomAD database, including 21,624 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 0.51 (21624 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77456 AN: 151750 Hom.: 21624 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.510 AC: 77471 AN: 151868 Hom.: 21624 Cov.: 31 AF XY: 0.507 AC XY: 37636 AN XY: 74222

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.528

Alfa AF: 0.614 Hom.: 39187

Bravo AF: 0.502

Asia WGS AF: 0.395 AC: 1372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.0
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1583830; hg19: chr7-154836010;