rs1598036

Variant names:

• chr2-5161020-C-T
• rs1598036

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• 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

African (AFR) AF: 0.0494 AC: 2045 AN: 41414

American (AMR) AF: 0.0522 AC: 797 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3462

East Asian (EAS) AF: 0.0452 AC: 234 AN: 5178

South Asian (SAS) AF: 0.0510 AC: 245 AN: 4804

European-Finnish (FIN) AF: 0.0399 AC: 419 AN: 10500

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0426 AC: 2895 AN: 67966

Other (OTH) AF: 0.0422 AC: 89 AN: 2108

Alfa AF: 0.0444 Hom.: 213

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
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1598036; hg19: chr2-5301153;