11-27737445-A-T

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, non coding transcript 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: ENST00000530663.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000530663.1	n.148-40923T>A		intron_variant, non_coding_transcript_variant		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;