13-23958899-C-A

Variant names:

• chr13-23958899-C-A
• rs4769296
• ENST00000655811.1:n.257+161C>A

Variant summary

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

The ENST00000655811.1(ENSG00000287530):​n.257+161C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,970 control chromosomes in the GnomAD database, including 11,034 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 (11034 hom., cov: 32)
• Consequence: ENSG00000287530 ENST00000655811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 1 publications found

Genes affected

ENSG00000287530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655811.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287530	ENST00000655811.1		n.257+161C>A		intron	N/A
	ENSG00000287530	ENST00000815603.1		n.164+4286C>A		intron	N/A
	ENSG00000287530	ENST00000815604.1		n.93+4355C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55085 AN: 151850 Hom.: 11029 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.363 AC: 55103 AN: 151970 Hom.: 11034 Cov.: 32 AF XY: 0.365 AC XY: 27104 AN XY: 74288

African (AFR) AF: 0.207 AC: 8582 AN: 41440

American (AMR) AF: 0.396 AC: 6043 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1307 AN: 3468

East Asian (EAS) AF: 0.165 AC: 853 AN: 5180

South Asian (SAS) AF: 0.363 AC: 1745 AN: 4810

European-Finnish (FIN) AF: 0.535 AC: 5648 AN: 10556

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29710 AN: 67938

Other (OTH) AF: 0.359 AC: 756 AN: 2104

Alfa AF: 0.417 Hom.: 7031

Bravo AF: 0.343

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.38
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs4769296; hg19: chr13-24533038;