rs6095722

Positions:

• chr20-37682226-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.1104A>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 0.176 in 151,096 control chromosomes in the GnomAD database, including 4,749 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 0.18 (4748 hom., cov: 31)
  • Exomes 𝑓: 0.057 (1 hom.)
• Consequence: LOC100287792 NR_040021.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100287792	NR_040021.1	n.1104A>G		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000373508.2	n.1107A>G		non_coding_transcript_exon_variant	4/4	2
	ENST00000655861.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26572 AN: 150704 Hom.: 4746 Cov.: 31

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0286

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.0974

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.155

GnomAD4 exome AF: 0.0567 AC: 17 AN: 300 Hom.: 1 Cov.: 0 AF XY: 0.0750 AC XY: 12 AN XY: 160

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0347

Gnomad4 NFE exome AF: 0.0446

Gnomad4 OTH exome AF: 0.136

GnomAD4 genome AF: 0.176 AC: 26611 AN: 150796 Hom.: 4748 Cov.: 31 AF XY: 0.172 AC XY: 12672 AN XY: 73572

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0286

Gnomad4 EAS AF: 0.0291

Gnomad4 SAS AF: 0.0337

Gnomad4 FIN AF: 0.0796

Gnomad4 NFE AF: 0.0654

Gnomad4 OTH AF: 0.154

Alfa AF: 0.129 Hom.: 569

Bravo AF: 0.190

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6095722; hg19: chr20-36310628;