1-172893799-C-T

Position:

• chr1-172893799-C-T

Variant summary

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

The ENST00000432694.2(ENSG00000224228):​n.224-110483C>T 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 0.321 in 151,998 control chromosomes in the GnomAD database, including 9,230 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 0.32 (9230 hom., cov: 32)
• Consequence: ENST00000432694.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000432694.2	n.224-110483C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48784 AN: 151880 Hom.: 9226 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.321 AC: 48805 AN: 151998 Hom.: 9230 Cov.: 32 AF XY: 0.330 AC XY: 24511 AN XY: 74284

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.324

Alfa AF: 0.274 Hom.: 6305

Bravo AF: 0.344

Asia WGS AF: 0.562 AC: 1954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489276; hg19: chr1-172862939;