rs13235325

Variant names:

• chr7-71100021-T-C
• rs13235325
• ENST00000785130.1:n.313-5388T>C

Variant summary

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

The ENST00000785130.1(ENSG00000302239):​n.313-5388T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,060 control chromosomes in the GnomAD database, including 4,966 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 0.23 (4966 hom., cov: 33)
• Consequence: ENSG00000302239 ENST00000785130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 2 publications found

Genes affected

ENSG00000302239 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785130.1. 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
	ENSG00000302239	ENST00000785130.1		n.313-5388T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35667 AN: 151942 Hom.: 4971 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.234 AC: 35657 AN: 152060 Hom.: 4966 Cov.: 33 AF XY: 0.232 AC XY: 17220 AN XY: 74298

African (AFR) AF: 0.108 AC: 4469 AN: 41564

American (AMR) AF: 0.213 AC: 3254 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3472

East Asian (EAS) AF: 0.00560 AC: 29 AN: 5178

South Asian (SAS) AF: 0.215 AC: 1030 AN: 4794

European-Finnish (FIN) AF: 0.269 AC: 2835 AN: 10550

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21693 AN: 67898

Other (OTH) AF: 0.272 AC: 574 AN: 2110

Alfa AF: 0.297 Hom.: 3488

Bravo AF: 0.226

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.85
PhyloP100		-1.5

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: rs13235325;

hg19: chr7-70565007;