chr1-207017819-G-A

Variant names:

• chr1-207017819-G-A
• rs12138969

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 0.14 in 152,206 control chromosomes in the GnomAD database, including 1,696 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 0.14 (1696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21303 AN: 152088 Hom.: 1683 Cov.: 32

Gnomad AFR AF: 0.0817

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0608

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.140 AC: 21354 AN: 152206 Hom.: 1696 Cov.: 32 AF XY: 0.140 AC XY: 10441 AN XY: 74420

African (AFR) AF: 0.0823 AC: 3419 AN: 41540

American (AMR) AF: 0.216 AC: 3305 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3470

East Asian (EAS) AF: 0.0605 AC: 313 AN: 5170

South Asian (SAS) AF: 0.103 AC: 497 AN: 4830

European-Finnish (FIN) AF: 0.164 AC: 1741 AN: 10598

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10742 AN: 67992

Other (OTH) AF: 0.187 AC: 394 AN: 2112

Alfa AF: 0.163 Hom.: 2825

Bravo AF: 0.140

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.70
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs12138969; hg19: chr1-207191164;