rs847428

Positions:

• chr7-16990328-C-A
• chr7-16990328-C-G
• chr7-16990328-C-T

Variant summary

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

The ENST00000685941.2(ENSG00000289189):​n.149C>A 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 0.117 in 152,222 control chromosomes in the GnomAD database, including 1,373 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 0.12 (1373 hom., cov: 32)
• Consequence: ENSG00000289189 ENST00000685941.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165

Genes affected

ENSG00000289189 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375170	XR_007060237.1	n.111C>A		non_coding_transcript_exon_variant	1/2
LOC105375170	XR_007060238.1	n.111C>A		non_coding_transcript_exon_variant	1/2
LOC124901595	XR_007060239.1	n.13494G>T		non_coding_transcript_exon_variant	4/4
LOC105375170	XR_927067.3	n.111C>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289189	ENST00000685941.2	n.149C>A		non_coding_transcript_exon_variant	1/2
ENSG00000289189	ENST00000687986.2	n.111C>A		non_coding_transcript_exon_variant	1/3
ENSG00000237773	ENST00000643090.1	n.307-18582G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17743 AN: 152104 Hom.: 1372 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.117 AC: 17746 AN: 152222 Hom.: 1373 Cov.: 32 AF XY: 0.117 AC XY: 8707 AN XY: 74414

Gnomad4 AFR AF: 0.0293

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.0396

Gnomad4 SAS AF: 0.0737

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0907 Hom.: 166

Bravo AF: 0.108

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs847428; hg19: chr7-17029952;