4-121076949-A-G

Variant names:

• chr4-121076949-A-G
• rs7694450
• ENST00000507782.1:n.267+3085A>G

Variant summary

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

The ENST00000507782.1(NDNF-AS1):​n.267+3085A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,078 control chromosomes in the GnomAD database, including 17,774 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 0.45 (17774 hom., cov: 32)
• Consequence: NDNF-AS1 ENST00000507782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 4 publications found

Genes affected

NDNF-AS1 (HGNC:55553): (NDNF antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.673 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507782.1. 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
	NDNF-AS1	NR_187407.1		n.334+3085A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NDNF-AS1	ENST00000507782.1	TSL:4	n.267+3085A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68057 AN: 151960 Hom.: 17775 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.448 AC: 68067 AN: 152078 Hom.: 17774 Cov.: 32 AF XY: 0.451 AC XY: 33552 AN XY: 74324

African (AFR) AF: 0.170 AC: 7068 AN: 41534

American (AMR) AF: 0.547 AC: 8348 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1337 AN: 3468

East Asian (EAS) AF: 0.692 AC: 3572 AN: 5162

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4808

European-Finnish (FIN) AF: 0.631 AC: 6671 AN: 10570

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37781 AN: 67968

Other (OTH) AF: 0.439 AC: 926 AN: 2108

Alfa AF: 0.502 Hom.: 4624

Bravo AF: 0.435

Asia WGS AF: 0.492 AC: 1705 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.78
PhyloP100		0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7694450;

hg19: chr4-121998104;