chr1-89065709-C-T

Variant names:

• chr1-89065709-C-T
• rs1536670
• ENST00000824610.1:n.178-2116C>T

Variant summary

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

The ENST00000824610.1(ENSG00000307222):​n.178-2116C>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 152,162 control chromosomes in the GnomAD database, including 45,183 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 (45183 hom., cov: 32)
• Consequence: ENSG00000307222 ENST00000824610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 3 publications found

Genes affected

ENSG00000307222 (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 (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378841	XR_947575.3	n.3208-2116C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307222	ENST00000824610.1	n.178-2116C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116813 AN: 152044 Hom.: 45140 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.768 AC: 116909 AN: 152162 Hom.: 45183 Cov.: 32 AF XY: 0.765 AC XY: 56911 AN XY: 74394

African (AFR) AF: 0.805 AC: 33398 AN: 41502

American (AMR) AF: 0.653 AC: 9986 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2645 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2908 AN: 5180

South Asian (SAS) AF: 0.780 AC: 3769 AN: 4830

European-Finnish (FIN) AF: 0.758 AC: 8021 AN: 10580

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53565 AN: 67996

Other (OTH) AF: 0.768 AC: 1620 AN: 2110

Alfa AF: 0.734 Hom.: 2571

Bravo AF: 0.760

Asia WGS AF: 0.708 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.69
PhyloP100		-1.2
PromoterAI		-0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1536670; hg19: chr1-89531392;