11-27737445-A-T

Variant names:

• chr11-27737445-A-T
• rs985205
• ENST00000530663.1:n.148-40923T>A

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.148-40923T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 152,026 control chromosomes in the GnomAD database, including 12,160 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 0.37 (12160 hom., cov: 32)
• Consequence: ENSG00000255496 ENST00000530663.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

Genes affected

ENSG00000255496 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 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.148-40923T>A		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55768 AN: 151908 Hom.: 12155 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.367 AC: 55796 AN: 152026 Hom.: 12160 Cov.: 32 AF XY: 0.364 AC XY: 27031 AN XY: 74298

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.370

Alfa AF: 0.297 Hom.: 920

Bravo AF: 0.347

Asia WGS AF: 0.334 AC: 1159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.74
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs985205; hg19: chr11-27758992;