1-22633861-C-G

Variant names:

• chr1-22633861-C-G
• rs665691

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 0.561 in 152,066 control chromosomes in the GnomAD database, including 25,728 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 0.56 (25728 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 20 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 (AFR) allele frequency at 95% confidence interval = 0.778 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: 0.560 AC: 85143 AN: 151948 Hom.: 25676 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.561 AC: 85247 AN: 152066 Hom.: 25728 Cov.: 33 AF XY: 0.566 AC XY: 42083 AN XY: 74306

African (AFR) AF: 0.785 AC: 32576 AN: 41514

American (AMR) AF: 0.562 AC: 8582 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1474 AN: 3464

East Asian (EAS) AF: 0.618 AC: 3198 AN: 5174

South Asian (SAS) AF: 0.665 AC: 3202 AN: 4816

European-Finnish (FIN) AF: 0.474 AC: 4996 AN: 10542

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29564 AN: 67964

Other (OTH) AF: 0.537 AC: 1135 AN: 2112

Alfa AF: 0.351 Hom.: 1075

Bravo AF: 0.576

Asia WGS AF: 0.660 AC: 2296 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	0.15
DANN	Benign	0.41
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs665691; hg19: chr1-22960354;