3-3344122-G-T

Variant names:

• chr3-3344122-G-T
• rs9861093
• ENST00000420000.6:n.374-6659C>A

Variant summary

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

The ENST00000455703.1(ENSG00000223727):​n.233-6659C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.082 in 152,086 control chromosomes in the GnomAD database, including 1,114 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 0.082 (1114 hom., cov: 32)
• Consequence: ENSG00000223727 ENST00000455703.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403
• Publications: 2 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455703.1. 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
	ENSG00000223727	ENST00000420000.6	TSL:4	n.374-6659C>A		intron	N/A
	ENSG00000223727	ENST00000451031.5	TSL:3	n.176-6659C>A		intron	N/A
	ENSG00000223727	ENST00000455703.1	TSL:2	n.233-6659C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12437 AN: 151968 Hom.: 1111 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0487

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0672

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

GnomAD4 genome AF: 0.0820 AC: 12472 AN: 152086 Hom.: 1114 Cov.: 32 AF XY: 0.0823 AC XY: 6119 AN XY: 74346

African (AFR) AF: 0.224 AC: 9269 AN: 41444

American (AMR) AF: 0.0487 AC: 745 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3470

East Asian (EAS) AF: 0.0841 AC: 435 AN: 5170

South Asian (SAS) AF: 0.0746 AC: 359 AN: 4812

European-Finnish (FIN) AF: 0.0305 AC: 323 AN: 10576

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0171 AC: 1161 AN: 68018

Other (OTH) AF: 0.0679 AC: 143 AN: 2106

Alfa AF: 0.0342 Hom.: 393

Bravo AF: 0.0902

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.71
PhyloP100		-0.40

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: rs9861093;

hg19: chr3-3385806;