rs1298190

Variant names:

• chr1-32874437-G-A
• rs1298190

Your query was ambiguous. Multiple possible variants found:

• chr1-32874437-G-A
• chr1-32874437-G-C
• chr1-32874437-G-T

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 0.824 in 151,992 control chromosomes in the GnomAD database, including 52,459 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 0.82 (52459 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.825 AC: 125233 AN: 151874 Hom.: 52449 Cov.: 30

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.890

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.824 AC: 125289 AN: 151992 Hom.: 52459 Cov.: 30 AF XY: 0.825 AC XY: 61323 AN XY: 74324

African (AFR) AF: 0.672 AC: 27796 AN: 41392

American (AMR) AF: 0.795 AC: 12131 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3109 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5167 AN: 5176

South Asian (SAS) AF: 0.927 AC: 4453 AN: 4804

European-Finnish (FIN) AF: 0.875 AC: 9260 AN: 10586

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.890 AC: 60478 AN: 67990

Other (OTH) AF: 0.851 AC: 1795 AN: 2110

Alfa AF: 0.877 Hom.: 25319

Bravo AF: 0.813

Asia WGS AF: 0.935 AC: 3249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.34
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1298190; hg19: chr1-33340038;