rs28542567

chr4-4931095-G-A

Variant summary

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

The NR_125893.1(LOC101928306):n.354-2725G>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 0.0473 in 152,120 control chromosomes in the GnomAD database, including 240 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 0.047 (240 hom., cov: 33)
• Consequence: LOC101928306 NR_125893.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394

Genes affected

LOC101928306 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928306	NR_125893.1	n.354-2725G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 7196 AN: 152004 Hom.: 239 Cov.: 33

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0370

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0397

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0659

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0473 AC: 7192 AN: 152120 Hom.: 240 Cov.: 33 AF XY: 0.0462 AC XY: 3433 AN XY: 74350

Gnomad4 AFR AF: 0.0103

Gnomad4 AMR AF: 0.0370

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.00425

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0397

Gnomad4 NFE AF: 0.0659

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0581 Hom.: 36

Bravo AF: 0.0430

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.5
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28542567; hg19: chr4-4932822;