rs1442460

Variant names:

• chr1-221114038-G-A
• rs1442460

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B.

Score: -12 - Benign

-12

BP4_StrongBA1

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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.490 AC: 20317 AN: 41424

American (AMR) AF: 0.455 AC: 6923 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1878 AN: 3466

East Asian (EAS) AF: 0.405 AC: 2091 AN: 5162

South Asian (SAS) AF: 0.390 AC: 1876 AN: 4812

European-Finnish (FIN) AF: 0.549 AC: 5790 AN: 10550

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39764 AN: 67934

Other (OTH) AF: 0.557 AC: 1176 AN: 2112

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

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