13-105999312-G-T

Position:

• chr13-105999312-G-T

Variant summary

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

The ENST00000657278.1(ENSG00000287923):​n.1796-46317C>A 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 0.601 in 151,952 control chromosomes in the GnomAD database, including 28,628 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 0.60 (28628 hom., cov: 31)
• Consequence: ENST00000657278.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657278.1	n.1796-46317C>A		intron_variant, non_coding_transcript_variant
	ENST00000670458.1	n.1563-46317C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91316 AN: 151834 Hom.: 28614 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.601 AC: 91360 AN: 151952 Hom.: 28628 Cov.: 31 AF XY: 0.589 AC XY: 43722 AN XY: 74276

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.0744

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.549

Alfa AF: 0.614 Hom.: 57348

Bravo AF: 0.594

Asia WGS AF: 0.313 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.54
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4996815; hg19: chr13-106651661;