chr7-145699048-A-G

Variant names:

• chr7-145699048-A-G
• rs850545

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;