chr1-183149147-T-C

Variant names:

• chr1-183149147-T-C
• rs2483675

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 0.814 in 152,090 control chromosomes in the GnomAD database, including 50,438 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 0.81 (50438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.883 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: 0.814 AC: 123739 AN: 151972 Hom.: 50403 Cov.: 32

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.814 AC: 123825 AN: 152090 Hom.: 50438 Cov.: 32 AF XY: 0.819 AC XY: 60874 AN XY: 74350

African (AFR) AF: 0.809 AC: 33526 AN: 41444

American (AMR) AF: 0.798 AC: 12197 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2955 AN: 3470

East Asian (EAS) AF: 0.904 AC: 4682 AN: 5178

South Asian (SAS) AF: 0.883 AC: 4247 AN: 4808

European-Finnish (FIN) AF: 0.853 AC: 9030 AN: 10592

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

European-Non Finnish (NFE) AF: 0.802 AC: 54499 AN: 67990

Other (OTH) AF: 0.816 AC: 1724 AN: 2114

Alfa AF: 0.808 Hom.: 119111

Bravo AF: 0.811

Asia WGS AF: 0.877 AC: 3049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.54
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2483675; hg19: chr1-183118282;