rs7048878

Positions:

• chr9-85783990-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657430.1(ENSG00000230303):​n.3868G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,060 control chromosomes in the GnomAD database, including 12,687 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 0.38 (12687 hom., cov: 32)
• Consequence: ENST00000657430.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGTPBP1	XM_047423086.1	c.-34+7497G>A		intron_variant			XP_047279042.1
AGTPBP1	XM_047423087.1	c.-34+7497G>A		intron_variant			XP_047279043.1
AGTPBP1	XM_047423088.1	c.-34+7497G>A		intron_variant			XP_047279044.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657430.1	n.3868G>A		non_coding_transcript_exon_variant	5/5
	ENST00000422653.1	n.1076-2114C>T		intron_variant, non_coding_transcript_variant
	ENST00000665432.1	n.3739G>A		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58044 AN: 151942 Hom.: 12659 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.382 AC: 58125 AN: 152060 Hom.: 12687 Cov.: 32 AF XY: 0.390 AC XY: 28973 AN XY: 74330

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.364

Alfa AF: 0.333 Hom.: 1570

Bravo AF: 0.395

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7048878; hg19: chr9-88398905;