rs850545

chr7-145699048-A-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 0.578 in 151,916 control chromosomes in the GnomAD database, including 26,122 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 0.58 (26122 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.671 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: 0.578 AC: 87671 AN: 151798 Hom.: 26089 Cov.: 31

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.578 AC: 87744 AN: 151916 Hom.: 26122 Cov.: 31 AF XY: 0.571 AC XY: 42365 AN XY: 74232

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.570

Alfa AF: 0.580 Hom.: 12423

Bravo AF: 0.574

Asia WGS AF: 0.317 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.6
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs850545; hg19: chr7-145396141;