rs16986255

Variant names:

• chr20-41903917-C-G
• rs16986255
• XR_001754609.2:n.69C>G

Variant summary

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

The XR_001754609.2(LOC101927182):​n.69C>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 0.0191 in 152,256 control chromosomes in the GnomAD database, including 135 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 0.019 (135 hom., cov: 32)
• Consequence: LOC101927182 XR_001754609.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

LOC101927182 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927182	XR_001754609.2	n.69C>G		non_coding_transcript_exon_variant	Exon 1 of 6
LOC101927182	XR_001754611.2	n.70C>G		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0191 AC: 2908 AN: 152136 Hom.: 136 Cov.: 32

Gnomad AFR AF: 0.00451

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.0158

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.00462

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.00454

Gnomad OTH AF: 0.0307

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0191 AC: 2907 AN: 152256 Hom.: 135 Cov.: 32 AF XY: 0.0205 AC XY: 1523 AN XY: 74466

Gnomad4 AFR AF: 0.00450

Gnomad4 AMR AF: 0.0951

Gnomad4 ASJ AF: 0.0158

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0164

Gnomad4 FIN AF: 0.00462

Gnomad4 NFE AF: 0.00454

Gnomad4 OTH AF: 0.0294

Alfa AF: 0.0119 Hom.: 8

Bravo AF: 0.0303

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	-0.80
CADD	Benign	2.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16986255; hg19: chr20-40532557;