rs3806808

Positions:

• chr4-119629930-A-C

Variant summary

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

The NR_165235.1(LOC107986192):​n.2141A>C 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 0.338 in 152,070 control chromosomes in the GnomAD database, including 8,750 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 0.34 (8750 hom., cov: 32)
• Consequence: LOC107986192 NR_165235.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

Genes affected

LOC107986192 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986192	NR_165235.1	n.2141A>C		non_coding_transcript_exon_variant	1/1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51393 AN: 151954 Hom.: 8731 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.338 AC: 51454 AN: 152070 Hom.: 8750 Cov.: 32 AF XY: 0.336 AC XY: 24965 AN XY: 74312

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.347

Alfa AF: 0.334 Hom.: 8058

Bravo AF: 0.347

Asia WGS AF: 0.293 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3806808; hg19: chr4-120551085;