rs7819928

chr8-71169443-C-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, non coding transcript 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: ENST00000521685.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000521685.5	n.167-6836C>A		intron_variant, non_coding_transcript_variant		3

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;