rs6057659

Variant names:

• chr20-32857341-G-A
• rs6057659
• ENST00000569087.2:n.721G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_171378.1(LOC119746555):​n.710G>A 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 0.0229 in 152,238 control chromosomes in the GnomAD database, including 56 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 0.023 (56 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LOC119746555 NR_171378.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

Genes affected

ENSG00000260257 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0229 (3480/152238) while in subpopulation SAS AF= 0.0439 (212/4824). AF 95% confidence interval is 0.0391. There are 56 homozygotes in gnomad4. There are 1722 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 56 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC119746555	NR_171378.1	n.710G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260257	ENST00000569087.2	n.721G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0228 AC: 3469 AN: 152120 Hom.: 55 Cov.: 31

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0163

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0229 AC: 3480 AN: 152238 Hom.: 56 Cov.: 31 AF XY: 0.0231 AC XY: 1722 AN XY: 74416

Gnomad4 AFR AF: 0.0371

Gnomad4 AMR AF: 0.0109

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0439

Gnomad4 FIN AF: 0.0162

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.0209 Hom.: 13

Bravo AF: 0.0216

Asia WGS AF: 0.0410 AC: 142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6057659; hg19: chr20-31445147;