13-40230195-G-T

Position:

• chr13-40230195-G-T

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 0.181 in 152,076 control chromosomes in the GnomAD database, including 2,702 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 0.18 (2702 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.40230195G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00598	ENST00000615947.1	n.47-12445C>A		intron_variant		4
LINC00598	ENST00000637438.1	n.401-23143C>A		intron_variant		5
LINC00598	ENST00000638084.1	n.406-12445C>A		intron_variant		5
LINC00598	ENST00000654662.1	n.553-29304C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27559 AN: 151958 Hom.: 2699 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.0853

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.181 AC: 27589 AN: 152076 Hom.: 2702 Cov.: 31 AF XY: 0.178 AC XY: 13233 AN XY: 74340

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.0848

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.176

Alfa AF: 0.167 Hom.: 2803

Bravo AF: 0.190

Asia WGS AF: 0.184 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9549123; hg19: chr13-40804332;