13-23951465-A-C

Variant names:

• chr13-23951465-A-C
• rs2147995
• ENST00000793729.1:n.204+2524T>G

Variant summary

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

The ENST00000793729.1(ENSG00000290660):​n.204+2524T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,120 control chromosomes in the GnomAD database, including 3,100 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 0.18 (3100 hom., cov: 32)
• Consequence: ENSG00000290660 ENST00000793729.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 2 publications found

Genes affected

ENSG00000290660 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793729.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290660	ENST00000793729.1		n.204+2524T>G		intron	N/A
	ENSG00000290660	ENST00000793731.1		n.221+2524T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27554 AN: 152002 Hom.: 3091 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.181 AC: 27587 AN: 152120 Hom.: 3100 Cov.: 32 AF XY: 0.185 AC XY: 13783 AN XY: 74366

African (AFR) AF: 0.128 AC: 5318 AN: 41508

American (AMR) AF: 0.379 AC: 5786 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1167 AN: 5144

South Asian (SAS) AF: 0.287 AC: 1379 AN: 4808

European-Finnish (FIN) AF: 0.0883 AC: 938 AN: 10622

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11497 AN: 67990

Other (OTH) AF: 0.209 AC: 441 AN: 2108

Alfa AF: 0.186 Hom.: 3982

Bravo AF: 0.200

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2147995; hg19: chr13-24525604;