rs16834456

chr1-192581407-C-A

Variant summary

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

The ENST00000644134.1(ENSG00000285280):n.468-12103G>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 0.151 in 152,030 control chromosomes in the GnomAD database, including 2,847 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 0.15 (2847 hom., cov: 32)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371664	XR_002958418.2	n.287+12192G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644134.1	n.468-12103G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22957 AN: 151912 Hom.: 2842 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.0479

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.151 AC: 22987 AN: 152030 Hom.: 2847 Cov.: 32 AF XY: 0.147 AC XY: 10948 AN XY: 74304

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.0861

Gnomad4 ASJ AF: 0.0479

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0758

Gnomad4 FIN AF: 0.0802

Gnomad4 NFE AF: 0.0844

Gnomad4 OTH AF: 0.111

Alfa AF: 0.118 Hom.: 224

Bravo AF: 0.161

Asia WGS AF: 0.0520 AC: 180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	11
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16834456; hg19: chr1-192550537;