rs16829458

Positions:

• chr1-192799194-G-A

Variant summary

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

The ENST00000644134.1(ENSG00000285280):​n.105-33000C>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 0.0828 in 152,106 control chromosomes in the GnomAD database, including 600 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 0.083 (600 hom., cov: 31)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 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
	ENST00000644134.1	n.105-33000C>T		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-33000C>T		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.200-6726C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0827 AC: 12569 AN: 151988 Hom.: 596 Cov.: 31

Gnomad AFR AF: 0.0703

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0754

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.0645

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.0828 AC: 12591 AN: 152106 Hom.: 600 Cov.: 31 AF XY: 0.0854 AC XY: 6351 AN XY: 74360

Gnomad4 AFR AF: 0.0707

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.0754

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.0645

Gnomad4 NFE AF: 0.0747

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0859 Hom.: 371

Bravo AF: 0.0820

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16829458; hg19: chr1-192768324;