rs12142165

Variant names:

• chr1-228195501-T-C
• rs12142165
• ENST00000805142.1:n.102+734T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-228195501-T-C
• chr1-228195501-T-G

Variant summary

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

The ENST00000805142.1(ENSG00000304651):​n.102+734T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,042 control chromosomes in the GnomAD database, including 7,314 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 0.30 (7314 hom., cov: 32)
• Consequence: ENSG00000304651 ENST00000805142.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 5 publications found

Genes affected

ENSG00000304651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805142.1. 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
	ENSG00000304651	ENST00000805142.1		n.102+734T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44909 AN: 151922 Hom.: 7311 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.295 AC: 44914 AN: 152042 Hom.: 7314 Cov.: 32 AF XY: 0.295 AC XY: 21961 AN XY: 74328

African (AFR) AF: 0.166 AC: 6880 AN: 41442

American (AMR) AF: 0.294 AC: 4493 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1903 AN: 5164

South Asian (SAS) AF: 0.519 AC: 2494 AN: 4806

European-Finnish (FIN) AF: 0.276 AC: 2923 AN: 10594

Middle Eastern (MID) AF: 0.414 AC: 120 AN: 290

European-Non Finnish (NFE) AF: 0.349 AC: 23739 AN: 67962

Other (OTH) AF: 0.319 AC: 674 AN: 2112

Alfa AF: 0.338 Hom.: 27553

Bravo AF: 0.290

Asia WGS AF: 0.441 AC: 1533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.60
PhyloP100		0.47

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: rs12142165;

hg19: chr1-228383202;