rs1060236

chr20-5474040-A-G

Variant summary

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

The NR_029405.1(LOC643406):n.705A>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 0.463 in 389,296 control chromosomes in the GnomAD database, including 34,973 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 0.48 (14308 hom., cov: 31)
  • Exomes 𝑓: 0.45 (20665 hom.)
• Consequence: LOC643406 NR_029405.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC643406	NR_029405.1	n.705A>G		non_coding_transcript_exon_variant	2/2
LOC107985411	XR_001754485.1	n.32+6196T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651499.1	n.1053A>G		non_coding_transcript_exon_variant	4/4
	ENST00000668553.1	n.1281-28507A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.477 AC: 68761 AN: 144262 Hom.: 14300 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.523

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.480

GnomAD4 exome AF: 0.454 AC: 111265 AN: 244922 Hom.: 20665 Cov.: 0 AF XY: 0.453 AC XY: 62356 AN XY: 137776

Gnomad4 AFR exome AF: 0.527

Gnomad4 AMR exome AF: 0.493

Gnomad4 ASJ exome AF: 0.557

Gnomad4 EAS exome AF: 0.267

Gnomad4 SAS exome AF: 0.454

Gnomad4 FIN exome AF: 0.471

Gnomad4 NFE exome AF: 0.450

Gnomad4 OTH exome AF: 0.462

GnomAD4 genome AF: 0.477 AC: 68806 AN: 144374 Hom.: 14308 Cov.: 31 AF XY: 0.477 AC XY: 33614 AN XY: 70426

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.474

Alfa AF: 0.476 Hom.: 1645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1060236; hg19: chr20-5454686;