chr13-37900250-G-A

Position:

• chr13-37900250-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 0.285 in 151,996 control chromosomes in the GnomAD database, including 6,747 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 0.28 (6747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43279 AN: 151878 Hom.: 6735 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.285 AC: 43317 AN: 151996 Hom.: 6747 Cov.: 32 AF XY: 0.290 AC XY: 21576 AN XY: 74300

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.277

Alfa AF: 0.275 Hom.: 9913

Bravo AF: 0.276

Asia WGS AF: 0.488 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4943543; hg19: chr13-38474387;