rs342096

chr2-20496496-G-T

Variant summary

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

The NR_157978.1(LOC107985856):n.359+4670C>A 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 0.258 in 152,150 control chromosomes in the GnomAD database, including 5,343 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 (5343 hom., cov: 32)
• Consequence: LOC107985856 NR_157978.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.912

Genes affected

LOC107985856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985856	NR_157978.1	n.359+4670C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39234 AN: 152032 Hom.: 5348 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.258 AC: 39245 AN: 152150 Hom.: 5343 Cov.: 32 AF XY: 0.255 AC XY: 18985 AN XY: 74380

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.0546

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.242

Alfa AF: 0.289 Hom.: 9502

Bravo AF: 0.247

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	9.0
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs342096; hg19: chr2-20696256;