13-39092096-T-C

Position:

• chr13-39092096-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655342.1(ENSG00000273507):​n.256+38768T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,048 control chromosomes in the GnomAD database, including 13,627 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 0.36 (13627 hom., cov: 32)
• Consequence: ENST00000655342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 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
	ENST00000655342.1	n.256+38768T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55381 AN: 151930 Hom.: 13595 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.365 AC: 55467 AN: 152048 Hom.: 13627 Cov.: 32 AF XY: 0.364 AC XY: 27079 AN XY: 74358

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.306

Alfa AF: 0.259 Hom.: 3276

Bravo AF: 0.385

Asia WGS AF: 0.409 AC: 1425 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2148418; hg19: chr13-39666233;