1-234590610-C-T

Variant names:

• chr1-234590610-C-T
• rs11581667
• ENST00000753986.1:n.116+4035G>A

Variant summary

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

The ENST00000753986.1(ENSG00000286210):​n.116+4035G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,068 control chromosomes in the GnomAD database, including 6,513 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 0.29 (6513 hom., cov: 32)
• Consequence: ENSG00000286210 ENST00000753986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 5 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=-0.93).
• 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: ENST00000753986.1. 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
	ENSG00000286210	ENST00000753986.1		n.116+4035G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43885 AN: 151950 Hom.: 6510 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.289 AC: 43908 AN: 152068 Hom.: 6513 Cov.: 32 AF XY: 0.284 AC XY: 21136 AN XY: 74310

African (AFR) AF: 0.260 AC: 10784 AN: 41480

American (AMR) AF: 0.247 AC: 3782 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3470

East Asian (EAS) AF: 0.219 AC: 1133 AN: 5174

South Asian (SAS) AF: 0.184 AC: 887 AN: 4824

European-Finnish (FIN) AF: 0.308 AC: 3249 AN: 10554

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21847 AN: 67960

Other (OTH) AF: 0.296 AC: 623 AN: 2108

Alfa AF: 0.252 Hom.: 2169

Bravo AF: 0.284

Asia WGS AF: 0.208 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.97
DANN	Benign	0.45
PhyloP100		-0.095

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: rs11581667;

hg19: chr1-234726356;

COSMIC: COSV66879230;