rs4943819

Positions:

• chr11-81232926-T-A
• chr11-81232926-T-C
• chr11-81232926-T-G

Variant summary

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

The ENST00000701193.1(ENSG00000287912):​n.114-41950T>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 0.526 in 151,514 control chromosomes in the GnomAD database, including 23,198 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 0.53 (23198 hom., cov: 32)
• Consequence: ENST00000701193.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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
	ENST00000701193.1	n.114-41950T>A		intron_variant, non_coding_transcript_variant
	ENST00000671134.1	n.324-41950T>A		intron_variant, non_coding_transcript_variant
	ENST00000671210.1	n.310-41950T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79540 AN: 151396 Hom.: 23141 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.526 AC: 79654 AN: 151514 Hom.: 23198 Cov.: 32 AF XY: 0.527 AC XY: 38975 AN XY: 74024

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.546

Alfa AF: 0.470 Hom.: 2273

Bravo AF: 0.556

Asia WGS AF: 0.739 AC: 2554 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4943819; hg19: chr11-80943969;