rs1491851

Variant names:

• chr11-27731216-T-C
• rs1491851
• ENST00000530663.1:n.148-34694A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-27731216-T-C
• chr11-27731216-T-G

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.148-34694A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,054 control chromosomes in the GnomAD database, including 14,797 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 0.41 (14797 hom., cov: 33)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 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
ENSG00000255496	ENST00000530663.1	n.148-34694A>G		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61768 AN: 151934 Hom.: 14794 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.406 AC: 61794 AN: 152054 Hom.: 14797 Cov.: 33 AF XY: 0.405 AC XY: 30067 AN XY: 74330

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.412

Alfa AF: 0.498 Hom.: 19346

Bravo AF: 0.384

Asia WGS AF: 0.359 AC: 1247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.37
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: rs1491851; hg19: chr11-27752763;