chr1-159711078-C-T

Variant names:

• chr1-159711078-C-T
• rs2808630
• ENST00000751816.1:n.108-15449C>T

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-15449C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 152,164 control chromosomes in the GnomAD database, including 45,128 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 0.77 (45128 hom., cov: 32)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 108 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751816.1. 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
	ENSG00000297913	ENST00000751816.1		n.108-15449C>T		intron	N/A
	ENSG00000297913	ENST00000751817.1		n.110-15449C>T		intron	N/A
	ENSG00000297913	ENST00000751818.1		n.63-15449C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116795 AN: 152046 Hom.: 45080 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.768 AC: 116903 AN: 152164 Hom.: 45128 Cov.: 32 AF XY: 0.770 AC XY: 57307 AN XY: 74390

African (AFR) AF: 0.835 AC: 34661 AN: 41530

American (AMR) AF: 0.797 AC: 12188 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2827 AN: 3472

East Asian (EAS) AF: 0.819 AC: 4237 AN: 5174

South Asian (SAS) AF: 0.673 AC: 3239 AN: 4816

European-Finnish (FIN) AF: 0.802 AC: 8472 AN: 10564

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48843 AN: 67990

Other (OTH) AF: 0.775 AC: 1638 AN: 2114

Alfa AF: 0.733 Hom.: 172362

Bravo AF: 0.773

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.47
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs2808630; hg19: chr1-159680868;