rs1598036

Variant names:

• chr2-5161020-C-T
• rs1598036

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.045 in 151,908 control chromosomes in the GnomAD database, including 160 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 0.045 (160 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.045 (6831/151908) while in subpopulation AMR AF= 0.0522 (797/15274). AF 95% confidence interval is 0.0492. There are 160 homozygotes in gnomad4. There are 3344 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 160 gene

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: 0.0448 AC: 6805 AN: 151790 Hom.: 158 Cov.: 32

Gnomad AFR AF: 0.0489

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0518

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0427

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

GnomAD4 genome AF: 0.0450 AC: 6831 AN: 151908 Hom.: 160 Cov.: 32 AF XY: 0.0450 AC XY: 3344 AN XY: 74240

Gnomad4 AFR AF: 0.0494

Gnomad4 AMR AF: 0.0522

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.0452

Gnomad4 SAS AF: 0.0510

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0426

Gnomad4 OTH AF: 0.0422

Alfa AF: 0.0436 Hom.: 43

Bravo AF: 0.0460

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
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: rs1598036; hg19: chr2-5301153;