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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745665.1. 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
	ENSG00000297128	ENST00000745665.1		n.228-1412C>A		intron	N/A
	ENSG00000297128	ENST00000745666.1		n.140-1412C>A		intron	N/A
	ENSG00000297128	ENST00000745667.1		n.189-1412C>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1412216;

hg19: chr1-56565917;