rs11915891

chr3-193770712-T-C

Variant summary

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

The ENST00000666648.1(ENSG00000286624):n.1363A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,098 control chromosomes in the GnomAD database, including 9,260 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 0.34 (9260 hom., cov: 33)
• Consequence: ENST00000666648.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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 (SAS) allele frequency at 95% confidence interval = 0.471 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
	ENST00000666648.1	n.1363A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51431 AN: 151978 Hom.: 9237 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.339 AC: 51512 AN: 152098 Hom.: 9260 Cov.: 33 AF XY: 0.342 AC XY: 25444 AN XY: 74362

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.320

Alfa AF: 0.283 Hom.: 6552

Bravo AF: 0.342

Asia WGS AF: 0.482 AC: 1656 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.48
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11915891; hg19: chr3-193488501;