13-23963862-A-G

Variant names:

• chr13-23963862-A-G
• rs7330124
• ENST00000655811.1:n.258-4778A>G

Variant summary

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

The ENST00000655811.1(ENSG00000287530):​n.258-4778A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,078 control chromosomes in the GnomAD database, including 8,320 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 0.32 (8320 hom., cov: 33)
• Consequence: ENSG00000287530 ENST00000655811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 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.258-4778A>G		intron	N/A
	ENSG00000287530	ENST00000815603.1		n.165-4778A>G		intron	N/A
	ENSG00000287530	ENST00000815604.1		n.94-4778A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49019 AN: 151960 Hom.: 8312 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.323 AC: 49064 AN: 152078 Hom.: 8320 Cov.: 33 AF XY: 0.321 AC XY: 23819 AN XY: 74310

African (AFR) AF: 0.316 AC: 13108 AN: 41466

American (AMR) AF: 0.249 AC: 3797 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3466

East Asian (EAS) AF: 0.0602 AC: 312 AN: 5184

South Asian (SAS) AF: 0.168 AC: 808 AN: 4816

European-Finnish (FIN) AF: 0.434 AC: 4580 AN: 10558

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24132 AN: 67992

Other (OTH) AF: 0.309 AC: 654 AN: 2114

Alfa AF: 0.359 Hom.: 1283

Bravo AF: 0.306

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.54
PhyloP100		-0.29

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: rs7330124;

hg19: chr13-24538001;