rs13307587

Variant names:

• chr7-13504104-A-G
• rs13307587
• ENST00000411542.1:n.352-132542A>G

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.352-132542A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,020 control chromosomes in the GnomAD database, including 4,947 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 (4947 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 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.352-132542A>G		intron	N/A
	ENSG00000229618	ENST00000638964.1	TSL:5	n.724-132542A>G		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.723-132542A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35014 AN: 151900 Hom.: 4945 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.230 AC: 35013 AN: 152020 Hom.: 4947 Cov.: 32 AF XY: 0.225 AC XY: 16702 AN XY: 74288

African (AFR) AF: 0.104 AC: 4323 AN: 41490

American (AMR) AF: 0.219 AC: 3337 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 928 AN: 3472

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5170

South Asian (SAS) AF: 0.0968 AC: 467 AN: 4824

European-Finnish (FIN) AF: 0.306 AC: 3225 AN: 10546

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21844 AN: 67934

Other (OTH) AF: 0.240 AC: 507 AN: 2110

Alfa AF: 0.286 Hom.: 22784

Bravo AF: 0.221

Asia WGS AF: 0.0620 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		0.046

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: rs13307587;

hg19: chr7-13543729;