rs10029715

Positions:

• chr4-186301446-T-C

Variant summary

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

The NR_033900.1(F11-AS1):​n.215-10414A>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 0.214 in 152,164 control chromosomes in the GnomAD database, including 3,733 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 0.21 (3733 hom., cov: 33)
• Consequence: F11-AS1 NR_033900.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587

Genes affected

F11-AS1 (HGNC:27725): (F11 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
F11-AS1	NR_033900.1	n.215-10414A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
F11-AS1	ENST00000505103.5	n.154-10414A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32532 AN: 152046 Hom.: 3728 Cov.: 33

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.214 AC: 32575 AN: 152164 Hom.: 3733 Cov.: 33 AF XY: 0.219 AC XY: 16285 AN XY: 74382

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.176

Alfa AF: 0.186 Hom.: 1171

Bravo AF: 0.218

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10029715; hg19: chr4-187222600;