ENST00000730408.1:n.2220A>G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901266	XR_007059465.1	n.4248+790T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295484	ENST00000730408.1	n.2220A>G		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000295484	ENST00000730409.1	n.2189A>G		non_coding_transcript_exon_variant	Exon 5 of 5
ENSG00000286277	ENST00000729876.1	n.74+6592T>C		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs2274822; hg19: chr6-14291089;