chr1-150580146-T-G

Variant names:

• chr1-150580146-T-G
• rs9803935
• ENST00000702780.2:n.318T>G

Variant summary

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

The ENST00000842747.1(ENSG00000290074):​n.101-7T>G variant causes a splice region, intron 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: ENSG00000290074 ENST00000842747.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95
• Publications: 14 publications found

Genes affected

ENSG00000290074 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842747.1. 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
	LOC107985203	NR_186817.1		n.317T>G		non_coding_transcript_exon	Exon 1 of 2
	LOC107985203	NR_186818.1		n.317T>G		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290074	ENST00000702780.2		n.318T>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000290074	ENST00000842744.1		n.385T>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000290074	ENST00000842745.1		n.385T>G		non_coding_transcript_exon	Exon 1 of 3

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

African (AFR) AF: 0.212 AC: 8768 AN: 41420

American (AMR) AF: 0.405 AC: 6168 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3468

East Asian (EAS) AF: 0.424 AC: 2185 AN: 5154

South Asian (SAS) AF: 0.323 AC: 1558 AN: 4820

European-Finnish (FIN) AF: 0.622 AC: 6536 AN: 10502

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37138 AN: 67908

Other (OTH) AF: 0.450 AC: 948 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	8.7
DANN	Benign	0.59
PhyloP100		2.0
PromoterAI		0.0082	Neutral

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: rs9803935;

hg19: chr1-150552622;