rs7415343

Positions:

• chr1-100611767-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;