rs16993280

chr22-22814988-G-A

Variant summary

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

The ENST00000686504.1(ENSG00000289120):n.208+3395C>T 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 0.146 in 151,166 control chromosomes in the GnomAD database, including 1,871 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 0.15 (1870 hom., cov: 31)
  • Exomes 𝑓: 0.11 (1 hom.)
• Consequence: ENST00000686504.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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
	ENST00000686504.1	n.208+3395C>T		intron_variant, non_coding_transcript_variant
	ENST00000702002.1	n.207+3395C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22001 AN: 150882 Hom.: 1871 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.0956

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.000406

Gnomad SAS AF: 0.0447

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.131

GnomAD4 exome AF: 0.111 AC: 20 AN: 180 Hom.: 1 AF XY: 0.0956 AC XY: 13 AN XY: 136

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.357

Gnomad4 NFE exome AF: 0.106

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.146 AC: 22006 AN: 150986 Hom.: 1870 Cov.: 31 AF XY: 0.142 AC XY: 10462 AN XY: 73704

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0955

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.000611

Gnomad4 SAS AF: 0.0452

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.129

Alfa AF: 0.138 Hom.: 221

Bravo AF: 0.147

Asia WGS AF: 0.0350 AC: 123 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.39
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16993280; hg19: chr22-23157485;