13-23955260-G-A

Variant names:

• chr13-23955260-G-A
• rs2765115
• ENST00000655811.1:n.121+647G>A

Variant summary

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

The ENST00000655811.1(ENSG00000287530):​n.121+647G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 146,920 control chromosomes in the GnomAD database, including 53,682 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 0.85 (53682 hom., cov: 21)
• Consequence: ENSG00000287530 ENST00000655811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287530	ENST00000655811.1		n.121+647G>A		intron	N/A
	ENSG00000287530	ENST00000815603.1		n.164+647G>A		intron	N/A
	ENSG00000287530	ENST00000815604.1		n.93+716G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.853 AC: 125265 AN: 146802 Hom.: 53664 Cov.: 21

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.836

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.853 AC: 125333 AN: 146920 Hom.: 53682 Cov.: 21 AF XY: 0.853 AC XY: 60830 AN XY: 71292

African (AFR) AF: 0.777 AC: 30494 AN: 39224

American (AMR) AF: 0.897 AC: 13146 AN: 14660

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2971 AN: 3438

East Asian (EAS) AF: 0.999 AC: 4839 AN: 4842

South Asian (SAS) AF: 0.957 AC: 4436 AN: 4634

European-Finnish (FIN) AF: 0.847 AC: 8179 AN: 9660

Middle Eastern (MID) AF: 0.833 AC: 235 AN: 282

European-Non Finnish (NFE) AF: 0.871 AC: 58560 AN: 67236

Other (OTH) AF: 0.860 AC: 1761 AN: 2048

Alfa AF: 0.865 Hom.: 160610

Bravo AF: 0.853

Asia WGS AF: 0.959 AC: 3331 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.35
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2765115;

hg19: chr13-24529399;