rs17076203

Positions:

• chr6-114544616-A-G

Variant summary

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

The ENST00000435802.2(ENSG00000226079):​n.52+628T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,238 control chromosomes in the GnomAD database, including 1,040 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 (1040 hom., cov: 32)
• Consequence: ENSG00000226079 ENST00000435802.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

Genes affected

ENSG00000226079 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LNCPOIR	NR_183487.1	n.77+628T>C		intron_variant
LNCPOIR	NR_183488.1	n.77+628T>C		intron_variant
LNCPOIR	NR_183489.1	n.77+628T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000226079	ENST00000435802.2	n.52+628T>C		intron_variant		3
ENSG00000226079	ENST00000652989.1	n.92+628T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17823 AN: 152120 Hom.: 1033 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.117 AC: 17854 AN: 152238 Hom.: 1040 Cov.: 32 AF XY: 0.119 AC XY: 8833 AN XY: 74418

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0868

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0896

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.109

Alfa AF: 0.119 Hom.: 1545

Bravo AF: 0.111

Asia WGS AF: 0.0950 AC: 329 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17076203; hg19: chr6-114865780;