chr1-159705927-T-C

Variant names:

• chr1-159705927-T-C
• rs876538
• ENST00000751816.1:n.108-20600T>C

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.108-20600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,100 control chromosomes in the GnomAD database, including 53,159 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 0.83 (53159 hom., cov: 30)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 24 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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
ENSG00000297913	ENST00000751816.1	n.108-20600T>C		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-20600T>C		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-20600T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126828 AN: 151982 Hom.: 53104 Cov.: 30

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.835 AC: 126946 AN: 152100 Hom.: 53159 Cov.: 30 AF XY: 0.836 AC XY: 62130 AN XY: 74346

African (AFR) AF: 0.870 AC: 36119 AN: 41494

American (AMR) AF: 0.881 AC: 13468 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2920 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5155 AN: 5164

South Asian (SAS) AF: 0.783 AC: 3769 AN: 4812

European-Finnish (FIN) AF: 0.830 AC: 8790 AN: 10586

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53929 AN: 67974

Other (OTH) AF: 0.845 AC: 1784 AN: 2110

Alfa AF: 0.816 Hom.: 12232

Bravo AF: 0.841

Asia WGS AF: 0.868 AC: 3018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.39
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs876538; hg19: chr1-159675717;