rs6886755

Variant names:

• chr5-111079903-G-T
• rs6886755
• ENST00000507269.3:n.213-2427C>A

Variant summary

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

The ENST00000507269.3(ENSG00000253613):​n.213-2427C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 152,222 control chromosomes in the GnomAD database, including 138 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 0.027 (138 hom., cov: 32)
• Consequence: ENSG00000253613 ENST00000507269.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

Genes affected

ENSG00000253613 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253613	ENST00000507269.3	n.213-2427C>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0273 AC: 4150 AN: 152104 Hom.: 134 Cov.: 32

Gnomad AFR AF: 0.0739

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.000864

Gnomad EAS AF: 0.0715

Gnomad SAS AF: 0.00830

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.000676

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0274 AC: 4171 AN: 152222 Hom.: 138 Cov.: 32 AF XY: 0.0280 AC XY: 2082 AN XY: 74408

Gnomad4 AFR AF: 0.0740

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.000864

Gnomad4 EAS AF: 0.0715

Gnomad4 SAS AF: 0.00789

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000676

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0200 Hom.: 11

Bravo AF: 0.0327

Asia WGS AF: 0.0380 AC: 131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6886755; hg19: chr5-110415601;