rs1555091

Variant names:

• chr6-127115500-G-A
• rs1555091
• ENST00000650648.1:n.402-44414C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-127115500-G-A
• chr6-127115500-G-C
• chr6-127115500-G-T

Variant summary

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

The ENST00000650648.1(ENSG00000286215):​n.402-44414C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,018 control chromosomes in the GnomAD database, including 7,536 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 0.31 (7536 hom., cov: 32)
• Consequence: ENSG00000286215 ENST00000650648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

Genes affected

ENSG00000286215 (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 (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377989	XR_002956387.2	n.3325+3401C>T		intron_variant	Intron 4 of 13
LOC105377989	XR_007059743.1	n.490-44414C>T		intron_variant	Intron 3 of 8
LOC105377989	XR_007059744.1	n.490-44414C>T		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286215	ENST00000650648.1	n.402-44414C>T		intron_variant	Intron 3 of 7
ENSG00000286215	ENST00000650684.1	n.474-44414C>T		intron_variant	Intron 3 of 8
ENSG00000286215	ENST00000650727.1	n.441-44414C>T		intron_variant	Intron 3 of 14

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46650 AN: 151900 Hom.: 7534 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.307 AC: 46673 AN: 152018 Hom.: 7536 Cov.: 32 AF XY: 0.308 AC XY: 22915 AN XY: 74304

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.306

Alfa AF: 0.252 Hom.: 2360

Bravo AF: 0.322

Asia WGS AF: 0.367 AC: 1280 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	14
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555091; hg19: chr6-127436645;