ENST00000807055.1:n.455+8080G>A

Variant names:

• chr6-111954157-G-A
• rs1327199
• ENST00000807055.1:n.455+8080G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000807055.1(ENSG00000289256):​n.455+8080G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 152,234 control chromosomes in the GnomAD database, including 480 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 0.055 (480 hom., cov: 32)
• Consequence: ENSG00000289256 ENST00000807055.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 2 publications found

Genes affected

ENSG00000289256 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 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
ENSG00000289256	ENST00000807055.1	n.455+8080G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0548 AC: 8336 AN: 152116 Hom.: 479 Cov.: 32

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0665

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.0288

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0548 AC: 8344 AN: 152234 Hom.: 480 Cov.: 32 AF XY: 0.0566 AC XY: 4216 AN XY: 74428

African (AFR) AF: 0.0966 AC: 4011 AN: 41520

American (AMR) AF: 0.0665 AC: 1017 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1396 AN: 5180

South Asian (SAS) AF: 0.0288 AC: 139 AN: 4830

European-Finnish (FIN) AF: 0.0205 AC: 217 AN: 10602

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0201 AC: 1368 AN: 68026

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0294 Hom.: 183

Bravo AF: 0.0613

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.36
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1327199; hg19: chr6-112275360;