chr1-206763900-G-T

Variant names:

• chr1-206763900-G-T
• rs6673928

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 0.196 in 152,156 control chromosomes in the GnomAD database, including 3,440 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 0.20 (3440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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: 0.196 AC: 29754 AN: 152036 Hom.: 3439 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.196 AC: 29756 AN: 152156 Hom.: 3440 Cov.: 32 AF XY: 0.190 AC XY: 14167 AN XY: 74386

African (AFR) AF: 0.118 AC: 4892 AN: 41522

American (AMR) AF: 0.153 AC: 2336 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 647 AN: 3470

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5182

South Asian (SAS) AF: 0.107 AC: 515 AN: 4826

European-Finnish (FIN) AF: 0.243 AC: 2566 AN: 10580

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18132 AN: 67982

Other (OTH) AF: 0.166 AC: 351 AN: 2110

Alfa AF: 0.229 Hom.: 1468

Bravo AF: 0.186

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.8
DANN	Benign	0.86
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6673928; hg19: chr1-206937245;