chr1-239233804-C-T

Variant names:

• chr1-239233804-C-T
• rs1339738

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 0.932 in 152,230 control chromosomes in the GnomAD database, including 66,233 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 0.93 (66233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.974 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: 0.932 AC: 141759 AN: 152112 Hom.: 66174 Cov.: 32

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.932 AC: 141874 AN: 152230 Hom.: 66233 Cov.: 32 AF XY: 0.933 AC XY: 69406 AN XY: 74426

African (AFR) AF: 0.982 AC: 40808 AN: 41550

American (AMR) AF: 0.947 AC: 14468 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3175 AN: 3472

East Asian (EAS) AF: 0.871 AC: 4501 AN: 5170

South Asian (SAS) AF: 0.891 AC: 4298 AN: 4824

European-Finnish (FIN) AF: 0.933 AC: 9897 AN: 10608

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61780 AN: 68010

Other (OTH) AF: 0.918 AC: 1941 AN: 2114

Alfa AF: 0.922 Hom.: 95694

Bravo AF: 0.936

Asia WGS AF: 0.878 AC: 3050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.81
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1339738; hg19: chr1-239397104;