chr1-199549877-G-A

Variant names:

• chr1-199549877-G-A
• rs945877

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 0.221 in 152,120 control chromosomes in the GnomAD database, including 4,052 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 0.22 (4052 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.55 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: 0.221 AC: 33646 AN: 152002 Hom.: 4053 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.221 AC: 33649 AN: 152120 Hom.: 4052 Cov.: 32 AF XY: 0.226 AC XY: 16791 AN XY: 74354

African (AFR) AF: 0.206 AC: 8545 AN: 41498

American (AMR) AF: 0.209 AC: 3187 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2926 AN: 5158

South Asian (SAS) AF: 0.237 AC: 1143 AN: 4832

European-Finnish (FIN) AF: 0.246 AC: 2602 AN: 10570

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13904 AN: 67994

Other (OTH) AF: 0.206 AC: 435 AN: 2112

Alfa AF: 0.207 Hom.: 1974

Bravo AF: 0.219

Asia WGS AF: 0.391 AC: 1357 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	0.95
DANN	Benign	0.77
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs945877; hg19: chr1-199519005; COSMIC: COSV60016563;