rs955612

Variant names:

• chr1-234580847-C-A
• rs955612
• ENST00000753986.1:n.116+13798G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-234580847-C-A
• chr1-234580847-C-T

Variant summary

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

The ENST00000753986.1(ENSG00000286210):​n.116+13798G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,052 control chromosomes in the GnomAD database, including 8,406 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 0.32 (8406 hom., cov: 33)
• Consequence: ENSG00000286210 ENST00000753986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 4 publications found

Genes affected

ENSG00000286210 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.424 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
ENSG00000286210	ENST00000753986.1	n.116+13798G>T		intron_variant	Intron 1 of 2
ENSG00000286210	ENST00000753987.1	n.149+3274G>T		intron_variant	Intron 1 of 1
ENSG00000286210	ENST00000753992.1	n.105+4850G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48786 AN: 151934 Hom.: 8394 Cov.: 33

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.321 AC: 48833 AN: 152052 Hom.: 8406 Cov.: 33 AF XY: 0.317 AC XY: 23592 AN XY: 74336

African (AFR) AF: 0.430 AC: 17813 AN: 41456

American (AMR) AF: 0.200 AC: 3056 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1288 AN: 5178

South Asian (SAS) AF: 0.210 AC: 1009 AN: 4816

European-Finnish (FIN) AF: 0.357 AC: 3782 AN: 10582

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20463 AN: 67954

Other (OTH) AF: 0.287 AC: 607 AN: 2112

Alfa AF: 0.297 Hom.: 22187

Bravo AF: 0.314

Asia WGS AF: 0.272 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.37
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs955612; hg19: chr1-234716593;