ENST00000664031.1:n.465+2619A>G

Variant names:

• chr1-118188432-A-G
• rs10494206
• ENST00000664031.1:n.465+2619A>G

Variant summary

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

The ENST00000664031.1(ENSG00000287980):​n.465+2619A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0475 in 152,330 control chromosomes in the GnomAD database, including 346 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 0.047 (346 hom., cov: 32)
• Consequence: ENSG00000287980 ENST00000664031.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340
• Publications: 1 publications found

Genes affected

ENSG00000287980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664031.1. 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
	ENSG00000287980	ENST00000664031.1		n.465+2619A>G		intron	N/A
	ENSG00000287980	ENST00000828985.1		n.580+2151A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0475 AC: 7225 AN: 152212 Hom.: 342 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0353

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0475 AC: 7231 AN: 152330 Hom.: 346 Cov.: 32 AF XY: 0.0484 AC XY: 3608 AN XY: 74496

African (AFR) AF: 0.0127 AC: 527 AN: 41580

American (AMR) AF: 0.0439 AC: 671 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1324 AN: 5182

South Asian (SAS) AF: 0.132 AC: 637 AN: 4830

European-Finnish (FIN) AF: 0.0353 AC: 375 AN: 10622

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0467 AC: 3177 AN: 68032

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.0442 Hom.: 87

Bravo AF: 0.0456

Asia WGS AF: 0.174 AC: 602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.2
DANN	Benign	0.83
PhyloP100		0.034

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: rs10494206;

hg19: chr1-118731055;