rs1442460

chr1-221114038-G-A

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 0.529 in 151,896 control chromosomes in the GnomAD database, including 21,697 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 0.53 (21697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 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: 0.529 AC: 80307 AN: 151778 Hom.: 21678 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.529 AC: 80366 AN: 151896 Hom.: 21697 Cov.: 32 AF XY: 0.524 AC XY: 38873 AN XY: 74248

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.557

Alfa AF: 0.565 Hom.: 4106

Bravo AF: 0.522

Asia WGS AF: 0.402 AC: 1395 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.1
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1442460; hg19: chr1-221287380; COSMIC: COSV60030457;