chr3-3462068-A-G

Variant names:

• chr3-3462068-A-G
• rs2218778
• ENST00000420000.6:n.201-79418T>C

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.201-79418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,082 control chromosomes in the GnomAD database, including 14,819 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 0.40 (14819 hom., cov: 33)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422
• Publications: 3 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420000.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223727	ENST00000420000.6	TSL:4	n.201-79418T>C		intron	N/A
	ENSG00000223727	ENST00000451031.5	TSL:3	n.78-21063T>C		intron	N/A
	ENSG00000223727	ENST00000455703.1	TSL:2	n.59+21971T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61244 AN: 151964 Hom.: 14805 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.403 AC: 61316 AN: 152082 Hom.: 14819 Cov.: 33 AF XY: 0.404 AC XY: 30041 AN XY: 74320

African (AFR) AF: 0.638 AC: 26482 AN: 41482

American (AMR) AF: 0.337 AC: 5150 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3464

East Asian (EAS) AF: 0.821 AC: 4247 AN: 5170

South Asian (SAS) AF: 0.377 AC: 1814 AN: 4810

European-Finnish (FIN) AF: 0.266 AC: 2810 AN: 10576

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18911 AN: 67998

Other (OTH) AF: 0.368 AC: 775 AN: 2106

Alfa AF: 0.307 Hom.: 12902

Bravo AF: 0.419

Asia WGS AF: 0.575 AC: 1996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.1
DANN	Benign	0.72
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs2218778; hg19: chr3-3503752;