rs939658

Positions:

• chr15-79159527-A-G

Variant summary

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

The variant allele was found at a frequency of 0.527 in 151,978 control chromosomes in the GnomAD database, including 21,403 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 0.53 (21403 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.79159527A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD34C-AS1	ENST00000671603.1	n.413+6090T>C		intron_variant
ANKRD34C-AS1	ENST00000685737.1	n.317-34841T>C		intron_variant
ANKRD34C-AS1	ENST00000689461.1	n.471+6090T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80018 AN: 151860 Hom.: 21371 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.527 AC: 80102 AN: 151978 Hom.: 21403 Cov.: 31 AF XY: 0.528 AC XY: 39230 AN XY: 74288

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.518

Alfa AF: 0.516 Hom.: 23908

Bravo AF: 0.545

Asia WGS AF: 0.405 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs939658; hg19: chr15-79451869;