1-200013982-G-C

Variant names:

• chr1-200013982-G-C
• rs2816937

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 0.19 in 152,040 control chromosomes in the GnomAD database, including 3,413 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 0.19 (3413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 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: 0.190 AC: 28851 AN: 151922 Hom.: 3404 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0291

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.190 AC: 28894 AN: 152040 Hom.: 3413 Cov.: 32 AF XY: 0.184 AC XY: 13677 AN XY: 74312

African (AFR) AF: 0.338 AC: 14014 AN: 41456

American (AMR) AF: 0.127 AC: 1930 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 401 AN: 3472

East Asian (EAS) AF: 0.0292 AC: 151 AN: 5170

South Asian (SAS) AF: 0.0789 AC: 380 AN: 4816

European-Finnish (FIN) AF: 0.122 AC: 1285 AN: 10576

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10176 AN: 67986

Other (OTH) AF: 0.183 AC: 387 AN: 2110

Alfa AF: 0.0802 Hom.: 99

Bravo AF: 0.196

Asia WGS AF: 0.0790 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.38
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs2816937; hg19: chr1-199983110;