1-199936700-C-T

Variant names:

• chr1-199936700-C-T
• rs12029406
• ENST00000703082.2:n.119-3193C>T

Variant summary

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

The ENST00000703082.2(ENSG00000290125):​n.119-3193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,920 control chromosomes in the GnomAD database, including 12,397 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 0.37 (12397 hom., cov: 31)
• Consequence: ENSG00000290125 ENST00000703082.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 12 publications found

Genes affected

ENSG00000290125 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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
ENSG00000290125	ENST00000703082.2	n.119-3193C>T		intron_variant	Intron 1 of 2
ENSG00000290125	ENST00000798203.1	n.103-3193C>T		intron_variant	Intron 1 of 2
ENSG00000290125	ENST00000798204.1	n.92-3193C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55746 AN: 151802 Hom.: 12389 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.423

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.367 AC: 55753 AN: 151920 Hom.: 12397 Cov.: 31 AF XY: 0.382 AC XY: 28379 AN XY: 74260

African (AFR) AF: 0.126 AC: 5219 AN: 41472

American (AMR) AF: 0.477 AC: 7274 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1345 AN: 3466

East Asian (EAS) AF: 0.765 AC: 3949 AN: 5160

South Asian (SAS) AF: 0.634 AC: 3060 AN: 4826

European-Finnish (FIN) AF: 0.512 AC: 5386 AN: 10524

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

European-Non Finnish (NFE) AF: 0.416 AC: 28243 AN: 67918

Other (OTH) AF: 0.371 AC: 784 AN: 2112

Alfa AF: 0.403 Hom.: 10256

Bravo AF: 0.351

Asia WGS AF: 0.620 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.77
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs12029406; hg19: chr1-199905828;