chr1-239233804-C-T

Position:

• chr1-239233804-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.982

Gnomad4 AMR AF: 0.947

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.918

Alfa AF: 0.912 Hom.: 59688

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1339738; hg19: chr1-239397104;