1-101398659-G-A

Variant names:

• chr1-101398659-G-A
• rs12403551
• ENST00000752250.1:n.215-855C>T

Variant summary

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

The ENST00000752250.1(ENSG00000297975):​n.215-855C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,380 control chromosomes in the GnomAD database, including 14,627 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 0.43 (14627 hom., cov: 31)
• Consequence: ENSG00000297975 ENST00000752250.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 2 publications found

Genes affected

ENSG00000297975 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752250.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297975	ENST00000752250.1		n.215-855C>T		intron	N/A
	ENSG00000297975	ENST00000752251.1		n.182-855C>T		intron	N/A
	ENSG00000297975	ENST00000752252.1		n.71-855C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65251 AN: 151262 Hom.: 14629 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.431 AC: 65267 AN: 151380 Hom.: 14627 Cov.: 31 AF XY: 0.433 AC XY: 32010 AN XY: 73886

African (AFR) AF: 0.307 AC: 12632 AN: 41202

American (AMR) AF: 0.498 AC: 7568 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1416 AN: 3464

East Asian (EAS) AF: 0.321 AC: 1649 AN: 5132

South Asian (SAS) AF: 0.512 AC: 2460 AN: 4804

European-Finnish (FIN) AF: 0.502 AC: 5225 AN: 10408

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32824 AN: 67868

Other (OTH) AF: 0.434 AC: 908 AN: 2092

Alfa AF: 0.460 Hom.: 69986

Bravo AF: 0.419

Asia WGS AF: 0.441 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.56
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs12403551; hg19: chr1-101864215;