chr1-30154865-C-T

Variant names:

• chr1-30154865-C-T
• rs2180233

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 0.779 in 152,128 control chromosomes in the GnomAD database, including 46,958 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 0.78 (46958 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.779 AC: 118479 AN: 152010 Hom.: 46912 Cov.: 31

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.779 AC: 118583 AN: 152128 Hom.: 46958 Cov.: 31 AF XY: 0.783 AC XY: 58186 AN XY: 74356

African (AFR) AF: 0.905 AC: 37576 AN: 41528

American (AMR) AF: 0.767 AC: 11723 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2503 AN: 3470

East Asian (EAS) AF: 0.997 AC: 5161 AN: 5178

South Asian (SAS) AF: 0.831 AC: 4004 AN: 4818

European-Finnish (FIN) AF: 0.716 AC: 7573 AN: 10576

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47574 AN: 67952

Other (OTH) AF: 0.763 AC: 1612 AN: 2114

Alfa AF: 0.749 Hom.: 45510

Bravo AF: 0.785

Asia WGS AF: 0.921 AC: 3198 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.60
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2180233; hg19: chr1-30627712;