rs842796

Positions:

• chr1-192933285-T-C

Variant summary

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

The ENST00000646606.1(ENSG00000285280):​n.295+14028A>G 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 0.616 in 151,990 control chromosomes in the GnomAD database, including 29,055 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 0.62 (29055 hom., cov: 32)
• Consequence: ENST00000646606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 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
	ENST00000646606.1	n.295+14028A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93538 AN: 151872 Hom.: 29012 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.616 AC: 93635 AN: 151990 Hom.: 29055 Cov.: 32 AF XY: 0.614 AC XY: 45567 AN XY: 74256

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.586

Alfa AF: 0.606 Hom.: 56678

Bravo AF: 0.619

Asia WGS AF: 0.587 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs842796; hg19: chr1-192902415; COSMIC: COSV71625402;