rs2817594

Variant names:

• chr1-11558535-T-G
• rs2817594

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 0.144 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.448 AC: 18506 AN: 41306

American (AMR) AF: 0.0631 AC: 963 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0669 AC: 232 AN: 3468

East Asian (EAS) AF: 0.0220 AC: 113 AN: 5140

South Asian (SAS) AF: 0.0443 AC: 213 AN: 4808

European-Finnish (FIN) AF: 0.00501 AC: 53 AN: 10586

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0219 AC: 1489 AN: 67968

Other (OTH) AF: 0.113 AC: 239 AN: 2108

Alfa AF: 0.0612 Hom.: 661

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2817594; hg19: chr1-11618592;