rs179853

Variant names:

• chr1-184980187-C-T
• rs179853

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 0.501 in 151,830 control chromosomes in the GnomAD database, including 19,755 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 0.50 (19755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 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: 0.501 AC: 75956 AN: 151712 Hom.: 19721 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.501 AC: 76045 AN: 151830 Hom.: 19755 Cov.: 32 AF XY: 0.495 AC XY: 36732 AN XY: 74204

African (AFR) AF: 0.585 AC: 24240 AN: 41404

American (AMR) AF: 0.448 AC: 6828 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1824 AN: 3466

East Asian (EAS) AF: 0.164 AC: 849 AN: 5178

South Asian (SAS) AF: 0.525 AC: 2532 AN: 4820

European-Finnish (FIN) AF: 0.396 AC: 4159 AN: 10510

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33748 AN: 67896

Other (OTH) AF: 0.480 AC: 1009 AN: 2104

Alfa AF: 0.493 Hom.: 7192

Bravo AF: 0.503

Asia WGS AF: 0.397 AC: 1385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.014
DANN	Benign	0.46
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs179853; hg19: chr1-184949319;