rs7819928

Variant names:

• chr8-71169443-C-A
• rs7819928
• ENST00000521685.5:n.167-6836C>A

Variant summary

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

The ENST00000521685.5(ENSG00000254031):​n.167-6836C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,984 control chromosomes in the GnomAD database, including 9,272 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 0.29 (9272 hom., cov: 32)
• Consequence: ENSG00000254031 ENST00000521685.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

ENSG00000254031 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 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
ENSG00000254031	ENST00000521685.5	n.167-6836C>A		intron_variant	Intron 2 of 5	3
ENSG00000285579	ENST00000647843.1	n.588-29697C>A		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44388 AN: 151866 Hom.: 9243 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.293 AC: 44462 AN: 151984 Hom.: 9272 Cov.: 32 AF XY: 0.288 AC XY: 21430 AN XY: 74292

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0990

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.240

Alfa AF: 0.191 Hom.: 4360

Bravo AF: 0.301

Asia WGS AF: 0.225 AC: 780 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	0.097
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7819928; hg19: chr8-72081678;