1-172645877-C-T

Variant names:

• chr1-172645877-C-T
• rs2859229

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 0.433 in 151,816 control chromosomes in the GnomAD database, including 14,299 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 0.43 (14299 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 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: 0.432 AC: 65606 AN: 151696 Hom.: 14273 Cov.: 31

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.433 AC: 65672 AN: 151816 Hom.: 14299 Cov.: 31 AF XY: 0.436 AC XY: 32356 AN XY: 74174

African (AFR) AF: 0.438 AC: 18124 AN: 41348

American (AMR) AF: 0.396 AC: 6050 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3466

East Asian (EAS) AF: 0.369 AC: 1904 AN: 5162

South Asian (SAS) AF: 0.547 AC: 2630 AN: 4806

European-Finnish (FIN) AF: 0.496 AC: 5221 AN: 10526

Middle Eastern (MID) AF: 0.403 AC: 117 AN: 290

European-Non Finnish (NFE) AF: 0.428 AC: 29053 AN: 67936

Other (OTH) AF: 0.427 AC: 899 AN: 2106

Alfa AF: 0.425 Hom.: 20202

Bravo AF: 0.418

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.54
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2859229; hg19: chr1-172615017;