1-152646068-A-T

Variant names:

• chr1-152646068-A-T
• rs989834
• ENST00000802896.1:n.421-1330T>A

Variant summary

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

The ENST00000802896.1(ENSG00000304363):​n.421-1330T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,026 control chromosomes in the GnomAD database, including 4,259 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 0.19 (4259 hom., cov: 32)
• Consequence: ENSG00000304363 ENST00000802896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 5 publications found

Genes affected

ENSG00000304363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 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
ENSG00000304363	ENST00000802896.1	n.421-1330T>A		intron_variant	Intron 3 of 3
ENSG00000304363	ENST00000802897.1	n.235-1330T>A		intron_variant	Intron 2 of 2
ENSG00000304363	ENST00000802898.1	n.198-1330T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29321 AN: 151908 Hom.: 4237 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.193 AC: 29378 AN: 152026 Hom.: 4259 Cov.: 32 AF XY: 0.196 AC XY: 14540 AN XY: 74312

African (AFR) AF: 0.396 AC: 16407 AN: 41412

American (AMR) AF: 0.160 AC: 2438 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1500 AN: 5160

South Asian (SAS) AF: 0.149 AC: 720 AN: 4822

European-Finnish (FIN) AF: 0.160 AC: 1688 AN: 10576

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0848 AC: 5762 AN: 67986

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.0697 Hom.: 100

Bravo AF: 0.202

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.36
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs989834; hg19: chr1-152618544;