1-56100245-G-T

Variant names:

• chr1-56100245-G-T
• rs1412216
• ENST00000745665.1:n.228-1412C>A

Variant summary

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

The ENST00000745665.1(ENSG00000297128):​n.228-1412C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,096 control chromosomes in the GnomAD database, including 5,712 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 0.25 (5712 hom., cov: 32)
• Consequence: ENSG00000297128 ENST00000745665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 1 publications found

Genes affected

ENSG00000297128 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378741	XR_001738063.2	n.228-1412C>A		intron_variant	Intron 1 of 2
LOC105378741	XR_001738064.2	n.166-1412C>A		intron_variant	Intron 1 of 2
LOC105378741	XR_001738065.2	n.228-1412C>A		intron_variant	Intron 1 of 3
LOC105378741	XR_001738066.2	n.228-1412C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297128	ENST00000745665.1	n.228-1412C>A		intron_variant	Intron 1 of 7
ENSG00000297128	ENST00000745666.1	n.140-1412C>A		intron_variant	Intron 1 of 9
ENSG00000297128	ENST00000745667.1	n.189-1412C>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37936 AN: 151978 Hom.: 5717 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.249 AC: 37928 AN: 152096 Hom.: 5712 Cov.: 32 AF XY: 0.248 AC XY: 18414 AN XY: 74358

African (AFR) AF: 0.0694 AC: 2880 AN: 41522

American (AMR) AF: 0.334 AC: 5100 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3468

East Asian (EAS) AF: 0.171 AC: 887 AN: 5180

South Asian (SAS) AF: 0.278 AC: 1340 AN: 4818

European-Finnish (FIN) AF: 0.280 AC: 2964 AN: 10578

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22648 AN: 67950

Other (OTH) AF: 0.295 AC: 623 AN: 2114

Alfa AF: 0.226 Hom.: 980

Bravo AF: 0.245

Asia WGS AF: 0.221 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	16
DANN	Benign	0.79
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1412216; hg19: chr1-56565917;