1-118188432-A-G

Position:

• chr1-118188432-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287980 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378930	XR_947745.3	n.584+2619A>G		intron_variant
LOC105378930	XR_947746.3	n.711+2151A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287980	ENST00000664031.1	n.465+2619A>G		intron_variant

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

Gnomad4 AFR AF: 0.0127

Gnomad4 AMR AF: 0.0439

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0353

Gnomad4 NFE AF: 0.0467

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0450 Hom.: 74

Bravo AF: 0.0456

Asia WGS AF: 0.174 AC: 602 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494206; hg19: chr1-118731055;