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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986770	XR_001745097.2	n.148-180346G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229618	ENST00000411542.1	n.352-114676G>A		intron_variant	Intron 3 of 4	4
ENSG00000229618	ENST00000638964.1	n.724-114676G>A		intron_variant	Intron 3 of 5	5
ENSG00000229618	ENST00000639998.1	n.723-114676G>A		intron_variant	Intron 5 of 7	5

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 v4.3

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

Other links and lift over

dbSNP: rs12699509; hg19: chr7-13561595;