rs1622146

chr1-231443426-T-C

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 0.319 in 152,020 control chromosomes in the GnomAD database, including 9,048 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 0.32 (9048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655

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 (AFR) allele frequency at 95% confidence interval = 0.496 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: 0.318 AC: 48378 AN: 151902 Hom.: 9021 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.319 AC: 48453 AN: 152020 Hom.: 9048 Cov.: 32 AF XY: 0.308 AC XY: 22888 AN XY: 74330

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0359

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.290

Alfa AF: 0.273 Hom.: 12090

Bravo AF: 0.344

Asia WGS AF: 0.113 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.9
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1622146; hg19: chr1-231579172;