13-21664523-C-G

Variant names:

• chr13-21664523-C-G
• rs263930
• ENST00000701135.2:n.277+6074G>C

Variant summary

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

The ENST00000701135.2(ENSG00000289860):​n.277+6074G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,078 control chromosomes in the GnomAD database, including 8,083 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 0.30 (8083 hom., cov: 32)
• Consequence: ENSG00000289860 ENST00000701135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 3 publications found

Genes affected

ENSG00000289860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.487 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
ENSG00000289860	ENST00000701135.2	n.277+6074G>C		intron_variant	Intron 2 of 2
ENSG00000289860	ENST00000753720.1	n.310+6074G>C		intron_variant	Intron 1 of 1
ENSG00000289860	ENST00000753721.1	n.352+6074G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44986 AN: 151960 Hom.: 8079 Cov.: 32

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.296 AC: 44997 AN: 152078 Hom.: 8083 Cov.: 32 AF XY: 0.306 AC XY: 22767 AN XY: 74346

African (AFR) AF: 0.0970 AC: 4026 AN: 41496

American (AMR) AF: 0.496 AC: 7579 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3470

East Asian (EAS) AF: 0.488 AC: 2511 AN: 5144

South Asian (SAS) AF: 0.354 AC: 1707 AN: 4822

European-Finnish (FIN) AF: 0.383 AC: 4044 AN: 10564

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22710 AN: 67982

Other (OTH) AF: 0.330 AC: 697 AN: 2112

Alfa AF: 0.189 Hom.: 438

Bravo AF: 0.294

Asia WGS AF: 0.380 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.64
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs263930; hg19: chr13-22238662;