1-168216936-C-T

Variant names:

• chr1-168216936-C-T
• rs12049577

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 0.578 in 120,556 control chromosomes in the GnomAD database, including 16,970 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 0.58 (16970 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.637 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: 0.578 AC: 69643 AN: 120466 Hom.: 16962 Cov.: 29

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.496

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.578 AC: 69669 AN: 120556 Hom.: 16970 Cov.: 29 AF XY: 0.576 AC XY: 33940 AN XY: 58874

African (AFR) AF: 0.444 AC: 12561 AN: 28272

American (AMR) AF: 0.577 AC: 6728 AN: 11658

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 1686 AN: 2814

East Asian (EAS) AF: 0.470 AC: 2129 AN: 4530

South Asian (SAS) AF: 0.453 AC: 1524 AN: 3364

European-Finnish (FIN) AF: 0.676 AC: 6364 AN: 9420

Middle Eastern (MID) AF: 0.483 AC: 113 AN: 234

European-Non Finnish (NFE) AF: 0.643 AC: 37189 AN: 57844

Other (OTH) AF: 0.546 AC: 909 AN: 1666

Alfa AF: 0.507 Hom.: 65877

Bravo AF: 0.442

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.80
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12049577; hg19: chr1-168186174;