1-22631825-T-C

Variant names:

• chr1-22631825-T-C
• rs587585

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.209 in 152,188 control chromosomes in the GnomAD database, including 4,296 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 0.21 (4296 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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: 0.209 AC: 31799 AN: 152070 Hom.: 4292 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.209 AC: 31835 AN: 152188 Hom.: 4296 Cov.: 33 AF XY: 0.209 AC XY: 15574 AN XY: 74430

African (AFR) AF: 0.382 AC: 15837 AN: 41484

American (AMR) AF: 0.132 AC: 2017 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3472

East Asian (EAS) AF: 0.142 AC: 736 AN: 5186

South Asian (SAS) AF: 0.208 AC: 1004 AN: 4816

European-Finnish (FIN) AF: 0.169 AC: 1793 AN: 10602

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9289 AN: 68010

Other (OTH) AF: 0.193 AC: 407 AN: 2114

Alfa AF: 0.168 Hom.: 5231

Bravo AF: 0.213

Asia WGS AF: 0.159 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.39
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs587585; hg19: chr1-22958318;