1-150580146-T-G

Position:

• chr1-150580146-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000702780.1(ENSG00000290074):​n.230T>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 0.43 in 151,808 control chromosomes in the GnomAD database, including 15,908 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 0.43 (15908 hom., cov: 31)
• Consequence: ENST00000702780.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985203	XR_001738230.3	n.317T>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000702780.1	n.230T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65248 AN: 151692 Hom.: 15914 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.430 AC: 65237 AN: 151808 Hom.: 15908 Cov.: 31 AF XY: 0.431 AC XY: 31973 AN XY: 74164

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.450

Alfa AF: 0.478 Hom.: 2318

Bravo AF: 0.404

Asia WGS AF: 0.399 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	8.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9803935; hg19: chr1-150552622;