1-219580167-T-C

Variant names:

• chr1-219580167-T-C
• rs2820443

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 0.232 in 152,126 control chromosomes in the GnomAD database, including 4,992 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 0.23 (4992 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.39 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: 0.232 AC: 35318 AN: 152008 Hom.: 4986 Cov.: 30

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.232 AC: 35333 AN: 152126 Hom.: 4992 Cov.: 30 AF XY: 0.236 AC XY: 17532 AN XY: 74344

African (AFR) AF: 0.0748 AC: 3108 AN: 41526

American (AMR) AF: 0.399 AC: 6095 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 820 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1368 AN: 5146

South Asian (SAS) AF: 0.230 AC: 1110 AN: 4822

European-Finnish (FIN) AF: 0.287 AC: 3037 AN: 10574

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19094 AN: 67974

Other (OTH) AF: 0.268 AC: 568 AN: 2116

Alfa AF: 0.263 Hom.: 10259

Bravo AF: 0.239

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	16
DANN	Benign	0.58
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs2820443; hg19: chr1-219753509; COSMIC: COSV60029500;