rs192709

Positions:

• chr4-111132270-T-G

Variant summary

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

The ENST00000681682.1(ENSG00000288692):​n.616+14998T>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 0.361 in 151,994 control chromosomes in the GnomAD database, including 10,413 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 0.36 (10413 hom., cov: 32)
• Consequence: ENST00000681682.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000681682.1	n.616+14998T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54830 AN: 151876 Hom.: 10407 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.361 AC: 54867 AN: 151994 Hom.: 10413 Cov.: 32 AF XY: 0.358 AC XY: 26605 AN XY: 74286

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.328

Alfa AF: 0.393 Hom.: 1477

Bravo AF: 0.347

Asia WGS AF: 0.314 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs192709; hg19: chr4-112053426;