rs4769296

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370115	XR_001749789.2	n.362+161C>A		intron_variant	Intron 3 of 4
LOC105370115	XR_001749790.2	n.359+161C>A		intron_variant	Intron 3 of 4
LOC105370115	XR_001749791.2	n.362+161C>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287530	ENST00000655811.1	n.257+161C>A		intron_variant	Intron 2 of 2
ENSG00000287530	ENST00000815603.1	n.164+4286C>A		intron_variant	Intron 1 of 1
ENSG00000287530	ENST00000815604.1	n.93+4355C>A		intron_variant	Intron 1 of 1

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 v4.3

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;