chr1-182620196-C-G

Variant names:

• chr1-182620196-C-G
• rs1287820

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 0.306 in 149,684 control chromosomes in the GnomAD database, including 8,629 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 0.31 (8629 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.367
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 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: 0.306 AC: 45741 AN: 149586 Hom.: 8594 Cov.: 29

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.306 AC: 45830 AN: 149684 Hom.: 8629 Cov.: 29 AF XY: 0.305 AC XY: 22257 AN XY: 72958

African (AFR) AF: 0.537 AC: 21940 AN: 40836

American (AMR) AF: 0.244 AC: 3693 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 506 AN: 3448

East Asian (EAS) AF: 0.346 AC: 1759 AN: 5088

South Asian (SAS) AF: 0.199 AC: 940 AN: 4730

European-Finnish (FIN) AF: 0.246 AC: 2386 AN: 9702

Middle Eastern (MID) AF: 0.192 AC: 55 AN: 286

European-Non Finnish (NFE) AF: 0.204 AC: 13785 AN: 67486

Other (OTH) AF: 0.250 AC: 520 AN: 2084

Alfa AF: 0.248 Hom.: 693

Bravo AF: 0.318

Asia WGS AF: 0.264 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.37
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1287820; hg19: chr1-182589331; COSMIC: COSV73690677;