chr4-186417181-C-T

Variant names:

• chr4-186417181-C-T
• rs11935103
• ENST00000505103.5:n.153+83664G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505103.5(F11-AS1):​n.153+83664G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,206 control chromosomes in the GnomAD database, including 5,413 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 0.26 (5413 hom., cov: 32)
• Consequence: F11-AS1 ENST00000505103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353
• Publications: 7 publications found

Genes affected

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

ENSG00000300494 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505103.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	NR_033900.1		n.214+83664G>A		intron	N/A
	F11-AS1	NR_033901.2		n.1573-845G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	F11-AS1	ENST00000505103.5	TSL:1	n.153+83664G>A		intron	N/A
	F11-AS1	ENST00000657917.1		n.347-38521G>A		intron	N/A
	F11-AS1	ENST00000771881.1		n.193-36759G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39977 AN: 152088 Hom.: 5411 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.263 AC: 40005 AN: 152206 Hom.: 5413 Cov.: 32 AF XY: 0.263 AC XY: 19539 AN XY: 74404

African (AFR) AF: 0.230 AC: 9540 AN: 41538

American (AMR) AF: 0.234 AC: 3573 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3468

East Asian (EAS) AF: 0.180 AC: 929 AN: 5170

South Asian (SAS) AF: 0.184 AC: 887 AN: 4828

European-Finnish (FIN) AF: 0.311 AC: 3296 AN: 10606

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19612 AN: 67980

Other (OTH) AF: 0.272 AC: 575 AN: 2114

Alfa AF: 0.271 Hom.: 16319

Bravo AF: 0.253

Asia WGS AF: 0.202 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.96
DANN	Benign	0.37
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs11935103; hg19: chr4-187338335;