13-39128618-A-G

Position:

• chr13-39128618-A-G

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 0.225 in 152,168 control chromosomes in the GnomAD database, including 4,275 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 0.23 (4275 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.427

Genes affected

(HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.39128618A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000273507	ENST00000614005.1	n.258-62985A>G		intron_variant		3
ENSG00000273507	ENST00000655342.1	n.257-62985A>G		intron_variant
ENSG00000273507	ENST00000668183.1	n.258-40773A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34248 AN: 152050 Hom.: 4269 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.225 AC: 34284 AN: 152168 Hom.: 4275 Cov.: 32 AF XY: 0.228 AC XY: 16976 AN XY: 74390

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.216

Alfa AF: 0.104 Hom.: 139

Bravo AF: 0.230

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1413042; hg19: chr13-39702755;