chr13-81467708-G-C

Variant names:

• chr13-81467708-G-C
• rs10507919
• ENST00000817144.1:n.192-766C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000817144.1(ENSG00000306348):​n.192-766C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0888 in 152,126 control chromosomes in the GnomAD database, including 1,675 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 0.089 (1675 hom., cov: 32)
• Consequence: ENSG00000306348 ENST00000817144.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 2 publications found

Genes affected

ENSG00000306348 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306348	ENST00000817144.1	n.192-766C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0887 AC: 13483 AN: 152008 Hom.: 1675 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0362

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0656

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00915

Gnomad OTH AF: 0.0647

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

GnomAD4 genome AF: 0.0888 AC: 13508 AN: 152126 Hom.: 1675 Cov.: 32 AF XY: 0.0865 AC XY: 6434 AN XY: 74378

African (AFR) AF: 0.282 AC: 11690 AN: 41466

American (AMR) AF: 0.0360 AC: 550 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00433 AC: 15 AN: 3468

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5170

South Asian (SAS) AF: 0.0655 AC: 316 AN: 4826

European-Finnish (FIN) AF: 0.0120 AC: 127 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00915 AC: 622 AN: 67998

Other (OTH) AF: 0.0682 AC: 144 AN: 2110

Alfa AF: 0.0522 Hom.: 124

Bravo AF: 0.0955

Asia WGS AF: 0.0600 AC: 209 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.63
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs10507919; hg19: chr13-82041843;