13-107914807-G-A

Position:

• chr13-107914807-G-A

Variant summary

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

The ENST00000663056.1(ENSG00000286343):​n.105-18221G>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 0.359 in 151,900 control chromosomes in the GnomAD database, including 10,266 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 (10266 hom., cov: 31)
• Consequence: ENST00000663056.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.845

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 (AMR) allele frequency at 95% confidence interval = 0.429 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
	ENST00000663056.1	n.105-18221G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54562 AN: 151784 Hom.: 10269 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.359 AC: 54572 AN: 151900 Hom.: 10266 Cov.: 31 AF XY: 0.356 AC XY: 26421 AN XY: 74228

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.381

Alfa AF: 0.403 Hom.: 9379

Bravo AF: 0.360

Asia WGS AF: 0.320 AC: 1115 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	8.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2940695; hg19: chr13-108567155;