chr1-182569906-C-G

Variant names:

• chr1-182569906-C-G
• rs635261

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 0.652 in 151,960 control chromosomes in the GnomAD database, including 32,900 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 0.65 (32900 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 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: 0.652 AC: 98949 AN: 151842 Hom.: 32872 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.652 AC: 99032 AN: 151960 Hom.: 32900 Cov.: 31 AF XY: 0.651 AC XY: 48397 AN XY: 74300

African (AFR) AF: 0.730 AC: 30251 AN: 41438

American (AMR) AF: 0.625 AC: 9556 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1675 AN: 3462

East Asian (EAS) AF: 0.345 AC: 1772 AN: 5142

South Asian (SAS) AF: 0.524 AC: 2521 AN: 4814

European-Finnish (FIN) AF: 0.745 AC: 7874 AN: 10568

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43456 AN: 67932

Other (OTH) AF: 0.635 AC: 1341 AN: 2112

Alfa AF: 0.569 Hom.: 1675

Bravo AF: 0.642

Asia WGS AF: 0.488 AC: 1698 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	2.3
DANN	Benign	0.57
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs635261; hg19: chr1-182539041;