rs1360558

Variant names:

• chr1-197024843-G-A
• rs1360558

Your query was ambiguous. Multiple possible variants found:

• chr1-197024843-G-A
• chr1-197024843-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 0.304 in 152,030 control chromosomes in the GnomAD database, including 8,820 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 0.30 (8820 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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: 0.305 AC: 46272 AN: 151912 Hom.: 8824 Cov.: 31

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.304 AC: 46270 AN: 152030 Hom.: 8820 Cov.: 31 AF XY: 0.300 AC XY: 22305 AN XY: 74288

Gnomad4 AFR AF: 0.0938

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.328

Alfa AF: 0.400 Hom.: 21470

Bravo AF: 0.286

Asia WGS AF: 0.202 AC: 704 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1360558; hg19: chr1-196993973; COSMIC: COSV60014250;