rs4075749

Variant names:

• chr3-30437405-A-G
• rs4075749
• ENST00000813897.1:n.1858A>G

Variant summary

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

The ENST00000813897.1(ENSG00000289450):​n.1858A>G 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 0.238 in 152,010 control chromosomes in the GnomAD database, including 4,828 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 0.24 (4828 hom., cov: 31)
• Consequence: ENSG00000289450 ENST00000813897.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 4 publications found

Genes affected

ENSG00000289450 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813897.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289450	ENST00000813897.1		n.1858A>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000289450	ENST00000691186.2		n.282-31628A>G		intron	N/A
	ENSG00000227549	ENST00000813769.1		n.399-15039T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36232 AN: 151892 Hom.: 4828 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.238 AC: 36229 AN: 152010 Hom.: 4828 Cov.: 31 AF XY: 0.235 AC XY: 17465 AN XY: 74278

African (AFR) AF: 0.130 AC: 5397 AN: 41488

American (AMR) AF: 0.241 AC: 3680 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1018 AN: 3468

East Asian (EAS) AF: 0.116 AC: 603 AN: 5178

South Asian (SAS) AF: 0.197 AC: 946 AN: 4814

European-Finnish (FIN) AF: 0.255 AC: 2699 AN: 10564

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 21025 AN: 67944

Other (OTH) AF: 0.248 AC: 524 AN: 2112

Alfa AF: 0.281 Hom.: 9231

Bravo AF: 0.231

Asia WGS AF: 0.135 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.28
DANN	Benign	0.23
PhyloP100		-0.60

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: rs4075749;

hg19: chr3-30478897;