1-22610601-T-G

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 0.191 in 151,892 control chromosomes in the GnomAD database, including 2,914 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 0.19 (2914 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.279 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: 0.191 AC: 28983 AN: 151776 Hom.: 2900 Cov.: 29

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.191 AC: 29039 AN: 151892 Hom.: 2914 Cov.: 29 AF XY: 0.193 AC XY: 14308 AN XY: 74244

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.191

Alfa AF: 0.198 Hom.: 6375

Bravo AF: 0.198

Asia WGS AF: 0.180 AC: 627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.15
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12128546; hg19: chr1-22937094;