1-39954009-A-G

Variant names:

• chr1-39954009-A-G
• rs3131703

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 0.694 in 152,000 control chromosomes in the GnomAD database, including 38,092 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 0.69 (38092 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.934
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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: 0.693 AC: 105319 AN: 151882 Hom.: 38030 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.686

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.978

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.694 AC: 105441 AN: 152000 Hom.: 38092 Cov.: 31 AF XY: 0.696 AC XY: 51687 AN XY: 74280

African (AFR) AF: 0.879 AC: 36454 AN: 41478

American (AMR) AF: 0.686 AC: 10474 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2115 AN: 3468

East Asian (EAS) AF: 0.978 AC: 5070 AN: 5182

South Asian (SAS) AF: 0.787 AC: 3794 AN: 4820

European-Finnish (FIN) AF: 0.561 AC: 5918 AN: 10554

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39745 AN: 67920

Other (OTH) AF: 0.659 AC: 1394 AN: 2114

Alfa AF: 0.642 Hom.: 13437

Bravo AF: 0.705

Asia WGS AF: 0.865 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs3131703; hg19: chr1-40419681;