11-49856729-T-C

Variant summary

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

The ENST00000532033.1(ENSG00000255550):n.158+990A>G 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 0.662 in 151,984 control chromosomes in the GnomAD database, including 33,831 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 0.66 (33831 hom., cov: 32)
• Consequence: ENST00000532033.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.751 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
	ENST00000532033.1	n.158+990A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100610 AN: 151866 Hom.: 33804 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.662 AC: 100679 AN: 151984 Hom.: 33831 Cov.: 32 AF XY: 0.664 AC XY: 49332 AN XY: 74288

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.713

Alfa AF: 0.669 Hom.: 4081

Bravo AF: 0.665

Asia WGS AF: 0.753 AC: 2620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.81
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7938734; hg19: chr11-49878281;