chr1-192600872-T-C

Position:

• chr1-192600872-T-C

Variant summary

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

The ENST00000434300.2(ENSG00000285280):​n.54-7215A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,994 control chromosomes in the GnomAD database, including 11,864 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 0.39 (11864 hom., cov: 32)
• Consequence: ENSG00000285280 ENST00000434300.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861

Genes affected

ENSG00000285280 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371664	XR_002958418.2	n.229-7215A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285280	ENST00000434300.2	n.54-7215A>G		intron_variant		5
ENSG00000285280	ENST00000642855.1	n.281-7215A>G		intron_variant
ENSG00000285280	ENST00000644058.1	n.498-7215A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58816 AN: 151878 Hom.: 11855 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.387 AC: 58847 AN: 151994 Hom.: 11864 Cov.: 32 AF XY: 0.394 AC XY: 29278 AN XY: 74286

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.400

Alfa AF: 0.398 Hom.: 1551

Bravo AF: 0.368

Asia WGS AF: 0.535 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489876; hg19: chr1-192570002;