chr20-46016700-G-A

Position:

• chr20-46016700-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NR_147699.1(SLC12A5-AS1):​n.669-1912C>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 0.158 in 348,140 control chromosomes in the GnomAD database, including 5,117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.15 (1923 hom., cov: 30)
  • Exomes 𝑓: 0.16 (3194 hom.)
• Consequence: SLC12A5-AS1 NR_147699.1 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.34

Genes affected

SLC12A5-AS1 (HGNC:53143): (SLC12A5 and MMP9 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 20-46016700-G-A is Benign according to our data. Variant chr20-46016700-G-A is described in ClinVar as [Benign]. Clinvar id is 1260772.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC12A5-AS1	NR_147699.1	n.669-1912C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC12A5-AS1	ENST00000535913.2	n.669-1912C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23435 AN: 151274 Hom.: 1925 Cov.: 30

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0933

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.161 AC: 31671 AN: 196754 Hom.: 3194 AF XY: 0.174 AC XY: 18727 AN XY: 107662

Gnomad4 AFR exome AF: 0.158

Gnomad4 AMR exome AF: 0.0740

Gnomad4 ASJ exome AF: 0.133

Gnomad4 EAS exome AF: 0.117

Gnomad4 SAS exome AF: 0.281

Gnomad4 FIN exome AF: 0.155

Gnomad4 NFE exome AF: 0.134

Gnomad4 OTH exome AF: 0.147

GnomAD4 genome AF: 0.155 AC: 23449 AN: 151386 Hom.: 1923 Cov.: 30 AF XY: 0.157 AC XY: 11577 AN XY: 73938

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.0930

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.154

Alfa AF: 0.160 Hom.: 278

Bravo AF: 0.147

Asia WGS AF: 0.206 AC: 713 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.99
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3918270; hg19: chr20-44645339;