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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.890

Gnomad4 OTH AF: 0.851

Alfa AF: 0.875 Hom.: 22271

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1298190; hg19: chr1-33340038;