13-38256214-G-A

Position:

• chr13-38256214-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 0.0337 in 152,220 control chromosomes in the GnomAD database, including 195 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 0.034 (195 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.0902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.38256214G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00571	ENST00000451826.2	n.323-28131C>T		intron_variant		2
LINC00571	ENST00000454060.2	n.323-28131C>T		intron_variant		3
LINC00571	ENST00000700975.1	n.305-28131C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0337 AC: 5119 AN: 152102 Hom.: 195 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00889

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0337 AC: 5134 AN: 152220 Hom.: 195 Cov.: 32 AF XY: 0.0328 AC XY: 2443 AN XY: 74420

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.0156

Gnomad4 ASJ AF: 0.0433

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0390

Gnomad4 FIN AF: 0.00292

Gnomad4 NFE AF: 0.00890

Gnomad4 OTH AF: 0.0241

Alfa AF: 0.0309 Hom.: 30

Bravo AF: 0.0360

Asia WGS AF: 0.0230 AC: 79 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
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: rs565738; hg19: chr13-38830351;