rs29228

Variant names:

• chr6-29655962-G-A
• rs29228
• ENST00000782059.1:n.43C>T

Variant summary

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

The ENST00000782059.1(ENSG00000301820):​n.43C>T 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 0.162 in 152,126 control chromosomes in the GnomAD database, including 2,405 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 0.16 (2405 hom., cov: 32)
• Consequence: ENSG00000301820 ENST00000782059.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 32 publications found

Genes affected

ENSG00000301820 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782059.1. 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
	ENSG00000301820	ENST00000782059.1		n.43C>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000301820	ENST00000782060.1		n.43C>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000301820	ENST00000782061.1		n.39C>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24622 AN: 152008 Hom.: 2392 Cov.: 32

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.162 AC: 24650 AN: 152126 Hom.: 2405 Cov.: 32 AF XY: 0.162 AC XY: 12060 AN XY: 74376

African (AFR) AF: 0.0667 AC: 2768 AN: 41526

American (AMR) AF: 0.176 AC: 2691 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3470

East Asian (EAS) AF: 0.326 AC: 1684 AN: 5168

South Asian (SAS) AF: 0.306 AC: 1478 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1313 AN: 10568

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13573 AN: 67992

Other (OTH) AF: 0.162 AC: 342 AN: 2108

Alfa AF: 0.185 Hom.: 4239

Bravo AF: 0.157

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	7.8
DANN	Benign	0.66
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs29228; hg19: chr6-29623739;