rs1351563

chr1-98851362-A-G

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 0.132 in 152,270 control chromosomes in the GnomAD database, including 1,555 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 0.13 (1555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20113 AN: 152152 Hom.: 1553 Cov.: 32

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.132 AC: 20116 AN: 152270 Hom.: 1555 Cov.: 32 AF XY: 0.131 AC XY: 9758 AN XY: 74442

Gnomad4 AFR AF: 0.0666

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.154

Alfa AF: 0.152 Hom.: 1295

Bravo AF: 0.135

Asia WGS AF: 0.168 AC: 583 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.7
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1351563; hg19: chr1-99316918;