rs1635135

Variant names:

• chr12-113017091-A-G
• rs1635135
• ENST00000552784.1:n.353+308T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-113017091-A-G
• chr12-113017091-A-T

Variant summary

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

The ENST00000552784.1(ENSG00000257452):​n.353+308T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,018 control chromosomes in the GnomAD database, including 4,222 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 0.22 (4222 hom., cov: 32)
• Consequence: ENSG00000257452 ENST00000552784.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 5 publications found

Genes affected

ENSG00000257452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257452	ENST00000552784.1	n.353+308T>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33707 AN: 151900 Hom.: 4224 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.222 AC: 33716 AN: 152018 Hom.: 4222 Cov.: 32 AF XY: 0.228 AC XY: 16941 AN XY: 74300

African (AFR) AF: 0.124 AC: 5135 AN: 41442

American (AMR) AF: 0.232 AC: 3547 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3464

East Asian (EAS) AF: 0.477 AC: 2462 AN: 5162

South Asian (SAS) AF: 0.330 AC: 1589 AN: 4814

European-Finnish (FIN) AF: 0.318 AC: 3366 AN: 10580

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16484 AN: 67970

Other (OTH) AF: 0.220 AC: 465 AN: 2112

Alfa AF: 0.237 Hom.: 2651

Bravo AF: 0.212

Asia WGS AF: 0.372 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.49
PhyloP100		-0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1635135; hg19: chr12-113454896;