rs12070116

Variant names:

• chr1-238280529-C-T
• rs12070116
• ENST00000422844.2:n.197+4370C>T

Variant summary

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

The ENST00000422844.2(ENSG00000234464):​n.197+4370C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0552 in 151,946 control chromosomes in the GnomAD database, including 637 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 0.055 (637 hom., cov: 32)
• Consequence: ENSG00000234464 ENST00000422844.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 1 publications found

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 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
ENSG00000234464	ENST00000422844.2	n.197+4370C>T		intron_variant	Intron 2 of 3	3
ENSG00000234464	ENST00000665394.1	n.193+4370C>T		intron_variant	Intron 2 of 4
ENSG00000234464	ENST00000716147.1	n.368+4370C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0552 AC: 8380 AN: 151830 Hom.: 638 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0235

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0233

Gnomad FIN AF: 0.00142

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.00936

Gnomad OTH AF: 0.0436

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

GnomAD4 genome AF: 0.0552 AC: 8392 AN: 151946 Hom.: 637 Cov.: 32 AF XY: 0.0534 AC XY: 3962 AN XY: 74238

African (AFR) AF: 0.172 AC: 7130 AN: 41422

American (AMR) AF: 0.0234 AC: 357 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3470

East Asian (EAS) AF: 0.00290 AC: 15 AN: 5178

South Asian (SAS) AF: 0.0238 AC: 114 AN: 4796

European-Finnish (FIN) AF: 0.00142 AC: 15 AN: 10532

Middle Eastern (MID) AF: 0.0241 AC: 7 AN: 290

European-Non Finnish (NFE) AF: 0.00934 AC: 635 AN: 67966

Other (OTH) AF: 0.0427 AC: 90 AN: 2110

Alfa AF: 0.0356 Hom.: 58

Bravo AF: 0.0617

Asia WGS AF: 0.0310 AC: 108 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.47
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs12070116; hg19: chr1-238443829;