chr7-13129230-T-C

Variant names:

• chr7-13129230-T-C
• rs758401
• ENST00000411542.1:n.112+27647T>C

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.112+27647T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,060 control chromosomes in the GnomAD database, including 61,072 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 0.90 (61072 hom., cov: 31)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705
• Publications: 2 publications found

Genes affected

ENSG00000229618 (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 (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411542.1. 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
	ENSG00000229618	ENST00000411542.1	TSL:4	n.112+27647T>C		intron	N/A
	ENSG00000229618	ENST00000638964.1	TSL:5	n.485-88315T>C		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.484-88315T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136084 AN: 151944 Hom.: 61007 Cov.: 31

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.896 AC: 136206 AN: 152060 Hom.: 61072 Cov.: 31 AF XY: 0.899 AC XY: 66834 AN XY: 74342

African (AFR) AF: 0.934 AC: 38775 AN: 41496

American (AMR) AF: 0.906 AC: 13843 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2905 AN: 3470

East Asian (EAS) AF: 0.926 AC: 4782 AN: 5164

South Asian (SAS) AF: 0.917 AC: 4420 AN: 4822

European-Finnish (FIN) AF: 0.922 AC: 9768 AN: 10592

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58819 AN: 67934

Other (OTH) AF: 0.880 AC: 1851 AN: 2104

Alfa AF: 0.883 Hom.: 10446

Bravo AF: 0.897

Asia WGS AF: 0.917 AC: 3179 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.78
DANN	Benign	0.79
PhyloP100		-0.70

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: rs758401;

hg19: chr7-13168855;