chr1-200968901-G-A

Variant names:

• chr1-200968901-G-A
• rs10494829

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 0.255 in 152,208 control chromosomes in the GnomAD database, including 5,858 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 0.25 (5858 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38777 AN: 152090 Hom.: 5860 Cov.: 33

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.255 AC: 38790 AN: 152208 Hom.: 5858 Cov.: 33 AF XY: 0.254 AC XY: 18877 AN XY: 74414

African (AFR) AF: 0.416 AC: 17263 AN: 41518

American (AMR) AF: 0.203 AC: 3107 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 609 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1569 AN: 5178

South Asian (SAS) AF: 0.115 AC: 555 AN: 4828

European-Finnish (FIN) AF: 0.247 AC: 2623 AN: 10602

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12391 AN: 68002

Other (OTH) AF: 0.229 AC: 483 AN: 2112

Alfa AF: 0.201 Hom.: 14726

Bravo AF: 0.260

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.024
DANN	Benign	0.69
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10494829; hg19: chr1-200938029;