ENST00000652300.1:n.491A>G

Variant names:

• chr1-208270177-T-C
• rs6670619
• ENST00000652300.1:n.491A>G

Variant summary

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

The ENST00000652300.1(ENSG00000286198):​n.491A>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 152,158 control chromosomes in the GnomAD database, including 5,357 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 (5357 hom., cov: 32)
• Consequence: ENSG00000286198 ENST00000652300.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• Publications: 1 publications found

Genes affected

ENSG00000286198 (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 = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904501	XR_007066852.1	n.473A>G		non_coding_transcript_exon_variant	Exon 1 of 2
LOC105372889	XR_922508.2	n.357+9402T>C		intron_variant	Intron 4 of 5
LOC105372889	XR_922509.2	n.354+9402T>C		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286198	ENST00000652300.1	n.491A>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000286198	ENST00000691549.3	n.467A>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000286198	ENST00000798438.1	n.467A>G		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37080 AN: 152040 Hom.: 5354 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.244 AC: 37085 AN: 152158 Hom.: 5357 Cov.: 32 AF XY: 0.240 AC XY: 17818 AN XY: 74376

African (AFR) AF: 0.127 AC: 5272 AN: 41520

American (AMR) AF: 0.202 AC: 3097 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1083 AN: 3462

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5182

South Asian (SAS) AF: 0.215 AC: 1037 AN: 4822

European-Finnish (FIN) AF: 0.283 AC: 2992 AN: 10564

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22418 AN: 67992

Other (OTH) AF: 0.255 AC: 539 AN: 2114

Alfa AF: 0.289 Hom.: 907

Bravo AF: 0.233

Asia WGS AF: 0.0940 AC: 328 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	2.3
DANN	Benign	0.43
PhyloP100		-0.076

Splicing

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

Other links and lift over

dbSNP: rs6670619; hg19: chr1-208443522; COSMIC: COSV60020187;