chr1-98087276-A-T

Variant names:

• chr1-98087276-A-T
• rs1198588
• ENST00000747811.1:n.125+32773A>T

Variant summary

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

The ENST00000747811.1(ENSG00000297419):​n.125+32773A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,032 control chromosomes in the GnomAD database, including 46,588 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 0.78 (46588 hom., cov: 31)
• Consequence: ENSG00000297419 ENST00000747811.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.29
• Publications: 59 publications found

Genes affected

ENSG00000297419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900404	XR_007066241.1	n.125+32773A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297419	ENST00000747811.1	n.125+32773A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118569 AN: 151914 Hom.: 46562 Cov.: 31

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.780 AC: 118639 AN: 152032 Hom.: 46588 Cov.: 31 AF XY: 0.781 AC XY: 58038 AN XY: 74294

African (AFR) AF: 0.721 AC: 29898 AN: 41468

American (AMR) AF: 0.851 AC: 12996 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3066 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4835 AN: 5156

South Asian (SAS) AF: 0.777 AC: 3742 AN: 4818

European-Finnish (FIN) AF: 0.737 AC: 7789 AN: 10562

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53680 AN: 67972

Other (OTH) AF: 0.785 AC: 1656 AN: 2110

Alfa AF: 0.799 Hom.: 27051

Bravo AF: 0.789

Asia WGS AF: 0.849 AC: 2954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.046
DANN	Benign	0.50
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs1198588; hg19: chr1-98552832;