chr1-39006382-G-C

Variant names:

• chr1-39006382-G-C
• rs999918

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 0.335 in 151,946 control chromosomes in the GnomAD database, including 9,138 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 0.33 (9138 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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: 0.335 AC: 50845 AN: 151828 Hom.: 9137 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.335 AC: 50858 AN: 151946 Hom.: 9138 Cov.: 32 AF XY: 0.331 AC XY: 24574 AN XY: 74268

African (AFR) AF: 0.273 AC: 11308 AN: 41434

American (AMR) AF: 0.285 AC: 4350 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3466

East Asian (EAS) AF: 0.118 AC: 612 AN: 5182

South Asian (SAS) AF: 0.132 AC: 636 AN: 4816

European-Finnish (FIN) AF: 0.454 AC: 4788 AN: 10550

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26796 AN: 67926

Other (OTH) AF: 0.338 AC: 714 AN: 2110

Alfa AF: 0.240 Hom.: 670

Bravo AF: 0.322

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.55
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs999918; hg19: chr1-39472054;