rs4696302

chr4-151891966-G-Achr4-151891966-G-Cchr4-151891966-G-T

Variant summary

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

The NR_183042.1(LOC127898557):n.383-29798G>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 0.276 in 152,142 control chromosomes in the GnomAD database, including 7,056 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 0.28 (7056 hom., cov: 33)
• Consequence: LOC127898557 NR_183042.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

LOC127898557 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC127898557	NR_183042.1	n.383-29798G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41898 AN: 152022 Hom.: 7058 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.276 AC: 41927 AN: 152142 Hom.: 7056 Cov.: 33 AF XY: 0.288 AC XY: 21433 AN XY: 74386

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.269

Alfa AF: 0.270 Hom.: 11850

Bravo AF: 0.277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.42
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4696302; hg19: chr4-152813118;