1-166339048-T-C

Position:

• chr1-166339048-T-C

Variant summary

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

The ENST00000653824.2(ENSG00000229588):​n.490T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,968 control chromosomes in the GnomAD database, including 18,541 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 0.46 (18541 hom., cov: 32)
• Consequence: ENST00000653824.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268276	XR_002958633.2	n.465T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653824.2	n.490T>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69954 AN: 151850 Hom.: 18500 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.461 AC: 70059 AN: 151968 Hom.: 18541 Cov.: 32 AF XY: 0.464 AC XY: 34501 AN XY: 74288

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.455

Alfa AF: 0.401 Hom.: 2291

Bravo AF: 0.487

Asia WGS AF: 0.572 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
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: rs7543540; hg19: chr1-166308285;