1-190872543-T-C

Variant names:

• chr1-190872543-T-C
• rs2053302

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 0.752 in 152,054 control chromosomes in the GnomAD database, including 44,406 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 0.75 (44406 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114331 AN: 151936 Hom.: 44380 Cov.: 33

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.752 AC: 114406 AN: 152054 Hom.: 44406 Cov.: 33 AF XY: 0.757 AC XY: 56249 AN XY: 74326

African (AFR) AF: 0.541 AC: 22400 AN: 41440

American (AMR) AF: 0.801 AC: 12209 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2919 AN: 3468

East Asian (EAS) AF: 0.927 AC: 4795 AN: 5172

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

European-Finnish (FIN) AF: 0.841 AC: 8909 AN: 10598

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56506 AN: 68010

Other (OTH) AF: 0.777 AC: 1634 AN: 2102

Alfa AF: 0.800 Hom.: 95808

Bravo AF: 0.736

Asia WGS AF: 0.837 AC: 2908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.66
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs2053302; hg19: chr1-190841673;