rs7363432

chr20-37678328-A-G

Variant summary

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

The NR_040021.1(LOC100287792):n.548A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0857 in 152,888 control chromosomes in the GnomAD database, including 721 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 0.086 (720 hom., cov: 32)
  • Exomes 𝑓: 0.089 (1 hom.)
• Consequence: LOC100287792 NR_040021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100287792	NR_040021.1	n.548A>G		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000373508.2	n.551A>G		non_coding_transcript_exon_variant	2/4	2
	ENST00000655861.1	n.199-12A>G		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13045 AN: 152220 Hom.: 720 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0318

Gnomad FIN AF: 0.0774

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.0933

GnomAD4 exome AF: 0.0891 AC: 49 AN: 550 Hom.: 1 Cov.: 0 AF XY: 0.0848 AC XY: 29 AN XY: 342

Gnomad4 AFR exome AF: 0.167

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0841

Gnomad4 NFE exome AF: 0.104

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0857 AC: 13053 AN: 152338 Hom.: 720 Cov.: 32 AF XY: 0.0848 AC XY: 6314 AN XY: 74498

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.0291

Gnomad4 SAS AF: 0.0321

Gnomad4 FIN AF: 0.0774

Gnomad4 NFE AF: 0.0639

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.0780 Hom.: 108

Bravo AF: 0.0880

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.37
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7363432; hg19: chr20-36306730;