1-203190998-G-T

Variant names:

• chr1-203190998-G-T
• rs4950929

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 0.841 in 152,196 control chromosomes in the GnomAD database, including 54,082 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 0.84 (54082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.840 AC: 127807 AN: 152078 Hom.: 54025 Cov.: 32

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.841 AC: 127924 AN: 152196 Hom.: 54082 Cov.: 32 AF XY: 0.841 AC XY: 62535 AN XY: 74394

African (AFR) AF: 0.920 AC: 38215 AN: 41550

American (AMR) AF: 0.880 AC: 13458 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3117 AN: 3470

East Asian (EAS) AF: 0.925 AC: 4795 AN: 5182

South Asian (SAS) AF: 0.837 AC: 4029 AN: 4816

European-Finnish (FIN) AF: 0.740 AC: 7834 AN: 10590

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53568 AN: 67972

Other (OTH) AF: 0.852 AC: 1802 AN: 2116

Alfa AF: 0.830 Hom.: 40301

Bravo AF: 0.856

Asia WGS AF: 0.868 AC: 3019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.16
DANN	Benign	0.39
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs4950929; hg19: chr1-203160126;