1-39985357-G-C

Variant names:

• chr1-39985357-G-C
• rs12083239

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 0.114 in 152,130 control chromosomes in the GnomAD database, including 1,248 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 0.11 (1248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17235 AN: 152012 Hom.: 1233 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.0575

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.114 AC: 17280 AN: 152130 Hom.: 1248 Cov.: 32 AF XY: 0.116 AC XY: 8658 AN XY: 74358

African (AFR) AF: 0.184 AC: 7633 AN: 41498

American (AMR) AF: 0.102 AC: 1565 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5172

South Asian (SAS) AF: 0.254 AC: 1222 AN: 4810

European-Finnish (FIN) AF: 0.0575 AC: 609 AN: 10584

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0682 AC: 4637 AN: 68006

Other (OTH) AF: 0.111 AC: 234 AN: 2110

Alfa AF: 0.0296 Hom.: 15

Bravo AF: 0.116

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.2
DANN	Benign	0.70
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12083239; hg19: chr1-40451029;