rs3811321

Positions:

• chr14-22013585-A-C
• chr14-22013585-A-G

Variant summary

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

The ENST00000553572.2(ENSG00000258705):​n.1676A>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0935 in 152,438 control chromosomes in the GnomAD database, including 991 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 0.094 (988 hom., cov: 28)
  • Exomes 𝑓: 0.077 (3 hom.)
• Consequence: ENST00000553572.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000553572.2	n.1676A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14177 AN: 151752 Hom.: 978 Cov.: 28

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0474

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0836

Gnomad EAS AF: 0.0488

Gnomad SAS AF: 0.0796

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.0868

GnomAD4 exome AF: 0.0775 AC: 44 AN: 568 Hom.: 3 Cov.: 0 AF XY: 0.0806 AC XY: 25 AN XY: 310

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.188

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0614

Gnomad4 OTH exome AF: 0.109

GnomAD4 genome AF: 0.0936 AC: 14216 AN: 151870 Hom.: 988 Cov.: 28 AF XY: 0.0909 AC XY: 6750 AN XY: 74250

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.0470

Gnomad4 ASJ AF: 0.0836

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.0799

Gnomad4 FIN AF: 0.0129

Gnomad4 NFE AF: 0.0623

Gnomad4 OTH AF: 0.0859

Alfa AF: 0.0665 Hom.: 231

Bravo AF: 0.0985

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.8
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3811321; hg19: chr14-22481824;