rs1872283

Variant names:

• chr8-106798663-G-A
• rs1872283
• ENST00000729376.1:n.120+8033C>T

Variant summary

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

The ENST00000729376.1(ENSG00000295337):​n.120+8033C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,158 control chromosomes in the GnomAD database, including 36,392 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 0.69 (36392 hom., cov: 33)
• Consequence: ENSG00000295337 ENST00000729376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 1 publications found

Genes affected

ENSG00000295337 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 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
ENSG00000295337	ENST00000729376.1	n.120+8033C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104305 AN: 152040 Hom.: 36353 Cov.: 33

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.686 AC: 104397 AN: 152158 Hom.: 36392 Cov.: 33 AF XY: 0.682 AC XY: 50693 AN XY: 74366

African (AFR) AF: 0.815 AC: 33836 AN: 41536

American (AMR) AF: 0.637 AC: 9742 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2589 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3548 AN: 5172

South Asian (SAS) AF: 0.618 AC: 2978 AN: 4822

European-Finnish (FIN) AF: 0.553 AC: 5840 AN: 10562

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.642 AC: 43615 AN: 67986

Other (OTH) AF: 0.710 AC: 1500 AN: 2112

Alfa AF: 0.663 Hom.: 136524

Bravo AF: 0.698

Asia WGS AF: 0.711 AC: 2472 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	0.0030
DANN	Benign	0.54
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1872283; hg19: chr8-107810891;