1-201179921-T-G

Variant names:

• chr1-201179921-T-G
• rs1404402

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 0.218 in 152,140 control chromosomes in the GnomAD database, including 4,314 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 0.22 (4314 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 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: 0.218 AC: 33147 AN: 152022 Hom.: 4310 Cov.: 32

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.218 AC: 33159 AN: 152140 Hom.: 4314 Cov.: 32 AF XY: 0.215 AC XY: 15982 AN XY: 74366

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.228

Alfa AF: 0.212 Hom.: 832

Bravo AF: 0.207

Asia WGS AF: 0.229 AC: 795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.096
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1404402; hg19: chr1-201149049;