rs342092

Positions:

• chr2-20498165-T-C

Variant summary

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

The NR_157978.1(LOC107985856):​n.359+3001A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,200 control chromosomes in the GnomAD database, including 5,450 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 0.26 (5450 hom., cov: 33)
• Consequence: LOC107985856 NR_157978.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

Genes affected

LOC107985856 (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 (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985856	NR_157978.1	n.359+3001A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39634 AN: 152082 Hom.: 5454 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0552

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.261 AC: 39652 AN: 152200 Hom.: 5450 Cov.: 33 AF XY: 0.258 AC XY: 19181 AN XY: 74402

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0549

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.248

Alfa AF: 0.292 Hom.: 7801

Bravo AF: 0.250

Asia WGS AF: 0.121 AC: 420 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	1.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342092; hg19: chr2-20697925;