rs1351563

Variant names:

• chr1-98851362-A-G
• rs1351563

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0666 AC: 2770 AN: 41570

American (AMR) AF: 0.195 AC: 2978 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1174 AN: 5170

South Asian (SAS) AF: 0.109 AC: 527 AN: 4830

European-Finnish (FIN) AF: 0.107 AC: 1134 AN: 10608

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10570 AN: 68022

Other (OTH) AF: 0.154 AC: 325 AN: 2114

Alfa AF: 0.152 Hom.: 1522

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
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs1351563; hg19: chr1-99316918;