rs2817594

Variant names:

• chr1-11558535-T-G
• rs2817594

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 0.144 in 151,844 control chromosomes in the GnomAD database, including 4,301 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 0.14 (4301 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

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 (AFR) allele frequency at 95% confidence interval = 0.443 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: 0.143 AC: 21769 AN: 151726 Hom.: 4291 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.00501

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.144 AC: 21832 AN: 151844 Hom.: 4301 Cov.: 31 AF XY: 0.140 AC XY: 10387 AN XY: 74210

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.0631

Gnomad4 ASJ AF: 0.0669

Gnomad4 EAS AF: 0.0220

Gnomad4 SAS AF: 0.0443

Gnomad4 FIN AF: 0.00501

Gnomad4 NFE AF: 0.0219

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0590 Hom.: 551

Bravo AF: 0.160

Asia WGS AF: 0.0680 AC: 237 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	2.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2817594; hg19: chr1-11618592;