chr4-151891966-G-A

Variant names:

• chr4-151891966-G-A
• rs4696302
• ENST00000716626.1:n.154-637C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183042.1(LOC127898557):​n.383-29798G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 3 publications found

Genes affected

ENSG00000249818 (HGNC:):

LINC03074 (HGNC:56654): (long intergenic non-protein coding RNA 3074)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183042.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC127898557	NR_183042.1		n.383-29798G>A		intron	N/A
	LOC102724700	NR_188364.1		n.264-637C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249818	ENST00000716626.1		n.154-637C>T		intron	N/A
	ENSG00000249818	ENST00000716627.1		n.275-637C>T		intron	N/A
	LINC03074	ENST00000731483.1		n.377-29798G>A		intron	N/A

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

African (AFR) AF: 0.153 AC: 6370 AN: 41518

American (AMR) AF: 0.393 AC: 6008 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1004 AN: 3468

East Asian (EAS) AF: 0.779 AC: 4024 AN: 5168

South Asian (SAS) AF: 0.368 AC: 1768 AN: 4800

European-Finnish (FIN) AF: 0.393 AC: 4168 AN: 10596

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17608 AN: 67990

Other (OTH) AF: 0.269 AC: 568 AN: 2110

Alfa AF: 0.268 Hom.: 18903

Bravo AF: 0.277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.38
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4696302; hg19: chr4-152813118;