rs16825275

Variant names:

• chr1-164140041-T-C
• rs16825275

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 0.0374 in 152,246 control chromosomes in the GnomAD database, including 502 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 0.037 (502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.487
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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: 0.0374 AC: 5687 AN: 152128 Hom.: 502 Cov.: 32

Gnomad AFR AF: 0.00647

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.0580

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0374 AC: 5693 AN: 152246 Hom.: 502 Cov.: 32 AF XY: 0.0424 AC XY: 3156 AN XY: 74430

African (AFR) AF: 0.00645 AC: 268 AN: 41574

American (AMR) AF: 0.0957 AC: 1463 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3472

East Asian (EAS) AF: 0.380 AC: 1960 AN: 5152

South Asian (SAS) AF: 0.0549 AC: 265 AN: 4826

European-Finnish (FIN) AF: 0.0580 AC: 615 AN: 10604

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0147 AC: 998 AN: 68022

Other (OTH) AF: 0.0403 AC: 85 AN: 2110

Alfa AF: 0.0365 Hom.: 60

Bravo AF: 0.0435

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.62
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs16825275; hg19: chr1-164109278;