rs7415343

Variant names:

• chr1-100611767-T-C
• rs7415343

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 0.687 in 150,896 control chromosomes in the GnomAD database, including 37,970 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 0.69 (37970 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.688 AC: 103672 AN: 150784 Hom.: 37953 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.687 AC: 103728 AN: 150896 Hom.: 37970 Cov.: 31 AF XY: 0.688 AC XY: 50803 AN XY: 73818

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.681

Alfa AF: 0.789 Hom.: 76539

Bravo AF: 0.670

Asia WGS AF: 0.795 AC: 2763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7415343; hg19: chr1-101077323;