chr1-201949399-T-G

Variant names:

• chr1-201949399-T-G
• rs2820304

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 0.321 in 151,962 control chromosomes in the GnomAD database, including 9,404 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 0.32 (9404 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48732 AN: 151844 Hom.: 9404 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.321 AC: 48739 AN: 151962 Hom.: 9404 Cov.: 32 AF XY: 0.319 AC XY: 23714 AN XY: 74268

African (AFR) AF: 0.128 AC: 5323 AN: 41478

American (AMR) AF: 0.245 AC: 3729 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3466

East Asian (EAS) AF: 0.195 AC: 1006 AN: 5158

South Asian (SAS) AF: 0.543 AC: 2617 AN: 4818

European-Finnish (FIN) AF: 0.400 AC: 4224 AN: 10568

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29666 AN: 67914

Other (OTH) AF: 0.294 AC: 620 AN: 2112

Alfa AF: 0.400 Hom.: 51533

Bravo AF: 0.292

Asia WGS AF: 0.335 AC: 1163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.84
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs2820304; hg19: chr1-201918527; COSMIC: COSV66172206;