rs7078219

Variant names:

• chr10-99514608-G-A
• rs7078219
• ENST00000806328.1:n.*33G>A

Variant summary

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

The ENST00000806328.1(ENSG00000304797):​n.*33G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,036 control chromosomes in the GnomAD database, including 11,343 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 (11343 hom., cov: 33)
• Consequence: ENSG00000304797 ENST00000806328.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 11 publications found

Genes affected

ENSG00000304797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.516 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
ENSG00000304797	ENST00000806328.1	n.*33G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57566 AN: 151918 Hom.: 11320 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.379 AC: 57633 AN: 152036 Hom.: 11343 Cov.: 33 AF XY: 0.386 AC XY: 28701 AN XY: 74280

African (AFR) AF: 0.303 AC: 12571 AN: 41476

American (AMR) AF: 0.453 AC: 6928 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1045 AN: 3468

East Asian (EAS) AF: 0.532 AC: 2751 AN: 5170

South Asian (SAS) AF: 0.380 AC: 1831 AN: 4818

European-Finnish (FIN) AF: 0.458 AC: 4818 AN: 10526

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26577 AN: 67970

Other (OTH) AF: 0.361 AC: 762 AN: 2112

Alfa AF: 0.387 Hom.: 50375

Bravo AF: 0.377

Asia WGS AF: 0.435 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.9
DANN	Benign	0.39
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs7078219; hg19: chr10-101274365;