1-192808677-G-C

Variant summary

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

The ENST00000644134.1(ENSG00000285280):n.105-42483C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,020 control chromosomes in the GnomAD database, including 6,588 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 0.29 (6588 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644134.1	n.105-42483C>G		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-42483C>G		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.200-16209C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44234 AN: 151902 Hom.: 6588 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.291 AC: 44250 AN: 152020 Hom.: 6588 Cov.: 32 AF XY: 0.291 AC XY: 21606 AN XY: 74292

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.280

Alfa AF: 0.140 Hom.: 253

Bravo AF: 0.291

Asia WGS AF: 0.392 AC: 1357 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.8
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2746072; hg19: chr1-192777807;