rs4234284

Variant names:

• chr3-127231283-G-A
• rs4234284
• ENST00000716127.1:n.112+3764G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-127231283-G-A
• chr3-127231283-G-C

Variant summary

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

The ENST00000716127.1(ENSG00000289641):​n.112+3764G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,118 control chromosomes in the GnomAD database, including 9,220 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 0.34 (9220 hom., cov: 33)
• Consequence: ENSG00000289641 ENST00000716127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 6 publications found

Genes affected

ENSG00000289641 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289641	ENST00000716127.1	n.112+3764G>A		intron_variant	Intron 1 of 2
ENSG00000289641	ENST00000826701.1	n.519+9423G>A		intron_variant	Intron 2 of 2
ENSG00000289641	ENST00000826702.1	n.126+3764G>A		intron_variant	Intron 1 of 1
ENSG00000289641	ENST00000826703.1	n.103-1817G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51844 AN: 152000 Hom.: 9219 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.341 AC: 51864 AN: 152118 Hom.: 9220 Cov.: 33 AF XY: 0.338 AC XY: 25109 AN XY: 74366

African (AFR) AF: 0.257 AC: 10658 AN: 41480

American (AMR) AF: 0.303 AC: 4636 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1236 AN: 5178

South Asian (SAS) AF: 0.326 AC: 1573 AN: 4824

European-Finnish (FIN) AF: 0.377 AC: 3982 AN: 10570

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27130 AN: 67988

Other (OTH) AF: 0.398 AC: 840 AN: 2108

Alfa AF: 0.380 Hom.: 16281

Bravo AF: 0.332

Asia WGS AF: 0.295 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.67
DANN	Benign	0.73
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs4234284; hg19: chr3-126950126;