rs7867029

Variant names:

• chr9-78405502-G-C
• rs7867029
• ENST00000832999.1:n.45-16592G>C

Variant summary

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

The ENST00000832999.1(ENSG00000308288):​n.45-16592G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,158 control chromosomes in the GnomAD database, including 4,776 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 0.21 (4776 hom., cov: 32)
• Consequence: ENSG00000308288 ENST00000832999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 7 publications found

Genes affected

ENSG00000308288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987083	XR_001746759.2	n.1049-16592G>C		intron_variant	Intron 1 of 3
LOC107987083	XR_001746760.2	n.1049-16592G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308288	ENST00000832999.1	n.45-16592G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32600 AN: 152040 Hom.: 4760 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0822

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.215 AC: 32650 AN: 152158 Hom.: 4776 Cov.: 32 AF XY: 0.212 AC XY: 15753 AN XY: 74404

African (AFR) AF: 0.416 AC: 17236 AN: 41470

American (AMR) AF: 0.196 AC: 2995 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1152 AN: 5174

South Asian (SAS) AF: 0.217 AC: 1049 AN: 4830

European-Finnish (FIN) AF: 0.0822 AC: 871 AN: 10602

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8313 AN: 67998

Other (OTH) AF: 0.199 AC: 420 AN: 2114

Alfa AF: 0.166 Hom.: 391

Bravo AF: 0.233

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.52
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs7867029; hg19: chr9-81020418;