chr1-16119854-G-A

Variant names:

• chr1-16119854-G-A
• rs924201

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 0.507 in 151,832 control chromosomes in the GnomAD database, including 22,161 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 0.51 (22161 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) 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: 0.508 AC: 77029 AN: 151714 Hom.: 22161 Cov.: 30

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.507 AC: 77033 AN: 151832 Hom.: 22161 Cov.: 30 AF XY: 0.508 AC XY: 37720 AN XY: 74204

African (AFR) AF: 0.218 AC: 9007 AN: 41366

American (AMR) AF: 0.530 AC: 8089 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1888 AN: 3464

East Asian (EAS) AF: 0.742 AC: 3825 AN: 5152

South Asian (SAS) AF: 0.514 AC: 2463 AN: 4792

European-Finnish (FIN) AF: 0.679 AC: 7171 AN: 10564

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43012 AN: 67918

Other (OTH) AF: 0.509 AC: 1072 AN: 2108

Alfa AF: 0.592 Hom.: 45454

Bravo AF: 0.486

Asia WGS AF: 0.533 AC: 1853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs924201; hg19: chr1-16446349;