rs1360558

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;