13-39111430-C-T

Position:

• chr13-39111430-C-T

Variant summary

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

The ENST00000655342.1(ENSG00000273507):​n.256+58102C>T 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 0.817 in 152,080 control chromosomes in the GnomAD database, including 52,526 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 0.82 (52526 hom., cov: 31)
• Consequence: ENST00000655342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367

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 (EAS) allele frequency at 95% confidence interval = 0.964 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+58102C>T		intron_variant, non_coding_transcript_variant
	ENST00000614005.1	n.257+58102C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000655935.1	n.286-7801C>T		intron_variant, non_coding_transcript_variant
	ENST00000668183.1	n.258-57961C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124212 AN: 151962 Hom.: 52511 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.817 AC: 124270 AN: 152080 Hom.: 52526 Cov.: 31 AF XY: 0.818 AC XY: 60822 AN XY: 74346

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.911

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.860

Alfa AF: 0.898 Hom.: 114570

Bravo AF: 0.809

Asia WGS AF: 0.906 AC: 3151 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	2.4
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409440; hg19: chr13-39685567;