6-14290858-T-C

Variant names:

• chr6-14290858-T-C
• rs2274822
• ENST00000730408.1:n.2220A>G

Variant summary

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

The ENST00000730408.1(ENSG00000295484):​n.2220A>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 0.244 in 152,138 control chromosomes in the GnomAD database, including 4,527 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 (4527 hom., cov: 32)
• Consequence: ENSG00000295484 ENST00000730408.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 4 publications found

Genes affected

ENSG00000295484 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730408.1. 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
	ENSG00000295484	ENST00000730408.1		n.2220A>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000295484	ENST00000730409.1		n.2189A>G		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000286277	ENST00000729876.1		n.74+6592T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37052 AN: 152020 Hom.: 4532 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.244 AC: 37047 AN: 152138 Hom.: 4527 Cov.: 32 AF XY: 0.244 AC XY: 18157 AN XY: 74344

African (AFR) AF: 0.211 AC: 8752 AN: 41528

American (AMR) AF: 0.227 AC: 3472 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1198 AN: 5176

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4820

European-Finnish (FIN) AF: 0.290 AC: 3065 AN: 10554

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17686 AN: 67972

Other (OTH) AF: 0.247 AC: 522 AN: 2114

Alfa AF: 0.258 Hom.: 6968

Bravo AF: 0.239

Asia WGS AF: 0.204 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.65
PhyloP100		0.013

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: rs2274822;

hg19: chr6-14291089;