rs1343295

Positions:

• chr1-166337516-T-C

Variant summary

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

The ENST00000653824.2(ENSG00000229588):​n.342-1384T>C 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 0.46 in 152,024 control chromosomes in the GnomAD database, including 18,531 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 (18531 hom., cov: 32)
• Consequence: ENST00000653824.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268276	XR_002958633.2	n.317-1384T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000653824.2	n.342-1384T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69870 AN: 151906 Hom.: 18487 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.460 AC: 69979 AN: 152024 Hom.: 18531 Cov.: 32 AF XY: 0.464 AC XY: 34462 AN XY: 74314

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.453

Alfa AF: 0.414 Hom.: 3444

Bravo AF: 0.486

Asia WGS AF: 0.574 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343295; hg19: chr1-166306753;