rs12699509

Variant names:

• chr7-13521970-G-A
• rs12699509
• ENST00000411542.1:n.352-114676G>A

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.352-114676G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 151,972 control chromosomes in the GnomAD database, including 3,876 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 0.21 (3876 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 4 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=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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.352-114676G>A		intron	N/A
	ENSG00000229618	ENST00000638964.1	TSL:5	n.724-114676G>A		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.723-114676G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31279 AN: 151854 Hom.: 3873 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0827

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.206 AC: 31290 AN: 151972 Hom.: 3876 Cov.: 32 AF XY: 0.201 AC XY: 14927 AN XY: 74262

African (AFR) AF: 0.108 AC: 4462 AN: 41442

American (AMR) AF: 0.194 AC: 2953 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5174

South Asian (SAS) AF: 0.0832 AC: 400 AN: 4810

European-Finnish (FIN) AF: 0.274 AC: 2888 AN: 10546

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.277 AC: 18829 AN: 67964

Other (OTH) AF: 0.223 AC: 471 AN: 2112

Alfa AF: 0.230 Hom.: 1206

Bravo AF: 0.198

Asia WGS AF: 0.0500 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.67
DANN	Benign	0.48
PhyloP100		-0.50

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: rs12699509;

hg19: chr7-13561595;