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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927995	XR_001740627.2	n.213-31628A>G		intron_variant	Intron 3 of 3
LOC101927995	XR_001740628.2	n.261-31628A>G		intron_variant	Intron 4 of 4
LOC101927995	XR_007095856.1	n.257-31628A>G		intron_variant	Intron 4 of 4
LOC105377013	XR_940683.2	n.293+3602T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289450	ENST00000813897.1	n.1858A>G		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000289450	ENST00000691186.2	n.282-31628A>G		intron_variant	Intron 3 of 3
ENSG00000227549	ENST00000813769.1	n.399-15039T>C		intron_variant	Intron 4 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs4075749; hg19: chr3-30478897;