rs7415619

Variant names:

• chr1-192962573-C-T
• rs7415619

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 0.0697 in 152,106 control chromosomes in the GnomAD database, including 453 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 0.070 (453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

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 (NFE) allele frequency at 95% confidence interval = 0.0932 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: 0.0697 AC: 10601 AN: 151988 Hom.: 453 Cov.: 32

Gnomad AFR AF: 0.0311

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0747

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0952

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0697 AC: 10608 AN: 152106 Hom.: 453 Cov.: 32 AF XY: 0.0689 AC XY: 5128 AN XY: 74376

Gnomad4 AFR AF: 0.0312

Gnomad4 AMR AF: 0.0803

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0259

Gnomad4 FIN AF: 0.0747

Gnomad4 NFE AF: 0.0952

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.0820 Hom.: 261

Bravo AF: 0.0708

Asia WGS AF: 0.0170 AC: 60 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	0.32
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7415619; hg19: chr1-192931703;