1-32290838-T-C

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 0.454 in 151,054 control chromosomes in the GnomAD database, including 18,753 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 0.45 (18753 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.996

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 (AFR) allele frequency at 95% confidence interval = 0.771 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: 0.453 AC: 68415 AN: 150940 Hom.: 18704 Cov.: 28

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.352

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.454 AC: 68515 AN: 151054 Hom.: 18753 Cov.: 28 AF XY: 0.454 AC XY: 33445 AN XY: 73674

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.407

Alfa AF: 0.333 Hom.: 9432

Bravo AF: 0.459

Asia WGS AF: 0.393 AC: 1369 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	3.0
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1741981; hg19: chr1-32756439;