1-38594823-G-A

Position:

• chr1-38594823-G-A

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 0.385 in 149,882 control chromosomes in the GnomAD database, including 11,555 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 0.39 (11555 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 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: 0.385 AC: 57716 AN: 149764 Hom.: 11542 Cov.: 26

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.385 AC: 57752 AN: 149882 Hom.: 11555 Cov.: 26 AF XY: 0.390 AC XY: 28484 AN XY: 73004

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.416

Alfa AF: 0.394 Hom.: 15837

Bravo AF: 0.388

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12026014; hg19: chr1-39060495;