chr7-50200973-A-G

Variant names:

• chr7-50200973-A-G
• rs1598702

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 0.761 in 152,132 control chromosomes in the GnomAD database, including 44,577 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 0.76 (44577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

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 (AMR) allele frequency at 95% confidence interval = 0.793 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: 0.760 AC: 115603 AN: 152012 Hom.: 44529 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.761 AC: 115716 AN: 152132 Hom.: 44577 Cov.: 32 AF XY: 0.761 AC XY: 56599 AN XY: 74392

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.764

Gnomad4 OTH AF: 0.737

Alfa AF: 0.772 Hom.: 5662

Bravo AF: 0.753

Asia WGS AF: 0.676 AC: 2355 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	2.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1598702; hg19: chr7-50240569;